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a/examples/child_strain_bf_comparison.csv b/examples/child_strain_bf_comparison.csv new file mode 100644 index 0000000..d1d7472 --- /dev/null +++ b/examples/child_strain_bf_comparison.csv @@ -0,0 +1,11 @@ +Model,log_Bayes_factor +serotype_specific_strain_modified_poisson,0 +serotype_specific_negbin,-5.59320690601498 +serotype_specific_strain_modified_negbin,-5.98567111588341 +serotype_specific_poisson,-24.6071372892982 +strain_specific_serotype_modified_poisson,-25.2688270257682 +strain_specific_serotype_modified_negbin,-29.9794458670223 +strain_and_serotype_specific_poisson,-33.292018864351 +strain_specific_negbin,-33.9402247131873 +strain_and_serotype_specific_negbin,-37.3258609345287 +strain_specific_poisson,-49.4616422980961 diff --git a/examples/child_strain_bf_sensitivity_comparison.csv b/examples/child_strain_bf_sensitivity_comparison.csv new file mode 100644 index 0000000..d1d7472 --- /dev/null +++ b/examples/child_strain_bf_sensitivity_comparison.csv @@ -0,0 +1,11 @@ +Model,log_Bayes_factor +serotype_specific_strain_modified_poisson,0 +serotype_specific_negbin,-5.59320690601498 +serotype_specific_strain_modified_negbin,-5.98567111588341 +serotype_specific_poisson,-24.6071372892982 +strain_specific_serotype_modified_poisson,-25.2688270257682 +strain_specific_serotype_modified_negbin,-29.9794458670223 +strain_and_serotype_specific_poisson,-33.292018864351 +strain_specific_negbin,-33.9402247131873 +strain_and_serotype_specific_negbin,-37.3258609345287 +strain_specific_poisson,-49.4616422980961 diff --git a/examples/child_strain_disease_loo_comparison.csv b/examples/child_strain_disease_loo_comparison.csv new file mode 100644 index 0000000..b0fa2f3 --- /dev/null +++ b/examples/child_strain_disease_loo_comparison.csv @@ -0,0 +1,11 @@ +,elpd_diff,se_diff,elpd_loo,se_elpd_loo,p_loo,se_p_loo,looic,se_looic +serotype_specific_strain_modified_poisson,0,0,-175.204625684994,8.39434076492268,43.5496207503873,3.16735054942898,350.409251369987,16.7886815298454 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+require(bridgesampling) +require(loo) +require(cowplot) +require(ggrepel) +require(xlsx) +require(gtools) +# Load stan package +library(progressionEstimation) + +################### +# Data structures # +################### + +# Define serotype categories and palettes +vaccine_types <- list( + "PCV7" = c("4","6B","9V","14","18C","19F","23F"), + "PCV10" = c("1","5","7F"), + "PCV13" = c("6A","3","19A"), + "PCV15" = c("22F","33F"), + "PCV20" = c("8","10A","11A","12F","15B/C"), + "PPV23" = c("2","9N","17F","20") +) + +vaccine_colours <- c("No PCV" = "blue", + "PCV7" = "red", + "PCV10" = "orange", + "PCV13" = "coral2", + "PCV15" = "pink", + "PCV20" = "purple", + "PPV23" = "black") + +epi_colors <- c( + "carriage" = "skyblue", + "disease" = "cornflowerblue" +) + +model_name_labels <- + c( + "type-specific Poisson", + "type-specific negative binomial", + "strain-specific Poisson", + "strain-specific negative binomial", + "type-specific strain-modified Poisson", + "type-specific strain-modified negative binomial", + "strain-specific type-modified Poisson", + "strain-specific type-modified negative binomial", + "strain- and type-specific Poisson", + "strain- and type-specific negative binomial" + ) + +``` + +## Read data + +Read in the adult and child progression rate estimates: + +```{r Read in data} + +infant_data <- read.csv("Dataset_S1.csv") %>% + dplyr::mutate("classification" = dplyr::case_when( + type %in% vaccine_types[["PCV7"]] ~ "PCV7", + type %in% vaccine_types[["PCV10"]] ~ "PCV10", + type %in% vaccine_types[["PCV13"]] ~ "PCV13", + type %in% vaccine_types[["PCV15"]] ~ "PCV15", + type %in% vaccine_types[["PCV20"]] ~ "PCV20", + type %in% vaccine_types[["PPV23"]] ~ "PPV23", + TRUE ~ "No PCV" + ) + ) %>% + dplyr::mutate(classification = factor(classification, levels = c("PCV7", + "PCV10", + "PCV13", + "PCV15", + "PCV20", + "PPV23", + "No PCV"))) +adult_data <- read.csv("Dataset_S2.csv") %>% + dplyr::mutate("classification" = dplyr::case_when( + type %in% vaccine_types[["PCV7"]] ~ "PCV7", + type %in% vaccine_types[["PCV10"]] ~ "PCV10", + type %in% vaccine_types[["PCV13"]] ~ "PCV13", + type %in% vaccine_types[["PCV15"]] ~ "PCV15", + type %in% vaccine_types[["PCV20"]] ~ "PCV20", + type %in% vaccine_types[["PPV23"]] ~ "PPV23", + TRUE ~ "No PCV" + ) + ) %>% + dplyr::mutate(classification = factor(classification, levels = c("PCV7", + "PCV10", + "PCV13", + "PCV15", + "PCV20", + "PPV23", + "No PCV"))) + +``` + +## Plot adult invasiveness + +Plot adult invasiveness: + +```{r Plot adult invasiveness} + +ggplot(adult_data, + aes(x = type, + y = invasiveness, + ymin = invasiveness_lower, + ymax = invasiveness_upper, + colour = classification)) + + geom_point() + + geom_errorbar() + + scale_colour_manual(values = vaccine_colours) + + scale_y_continuous(trans = "log10") + + scale_shape_binned(name = "Number of\nisolates", + breaks = c(5,10,25,50,100)) + + theme_bw() + +(adult_invasiveness_plot <- + progressionEstimation::plot_progression_rates(adult_data, + unit_time = "year", + type_name = "Serotype", + colour_col = "classification", + colour_palette = vaccine_colours, + use_sample_size = TRUE)) + +``` + +## Plot invasiveness comparison + +Plot the comparison: + +``` {r Plot comparison} + +joint_invasiveness <- + adult_data %>% + dplyr::left_join( + infant_data %>% + dplyr::rename(infant_nu = nu) %>% + dplyr::rename(infant_nu_lower = nu_lower) %>% + dplyr::rename(infant_nu_upper = nu_upper) + ) + +ggplot(joint_invasiveness, + aes( + x = nu, + y = infant_nu, + xmin = nu_lower, + xmax = nu_upper, + ymin = infant_nu_lower, + ymax = infant_nu_upper, + colour = classification + ) + ) + + geom_point() + + xlab("Progression rate estimate in adults (disease per carrier per year)") + + ylab("Progression rate estimate in infants (disease per carrier per year)") + +``` \ No newline at end of file diff --git a/examples/infant_combined_rhat_plots.pdf b/examples/infant_combined_rhat_plots.pdf 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b/examples/netherlands_or_comparison.png differ diff --git a/examples/s-pneumoniae-serotype-invasiveness-adults.Rmd b/examples/s-pneumoniae-serotype-invasiveness-adults.Rmd index 6420673..1c01320 100644 --- a/examples/s-pneumoniae-serotype-invasiveness-adults.Rmd +++ b/examples/s-pneumoniae-serotype-invasiveness-adults.Rmd @@ -29,8 +29,8 @@ require(xlsx) # Load stan package library(progressionEstimation) -pkgbuild::compile_dll() -roxygen2::roxygenize(package.dir = "..") +#pkgbuild::compile_dll() +#roxygen2::roxygenize(package.dir = "..") # Define serotype categories and palettes vaccine_types <- list( @@ -55,6 +55,17 @@ epi_colors <- c( "disease" = "cornflowerblue" ) +model_name_labels <- + c("null Poisson", + "null negative binomial", + "type-specific Poisson", + "type-specific negative binomial", + "study-adjusted Poisson", + "study-adjusted negative binomial", + "study-adjusted type-specific Poisson", + "study-adjusted type-specific negative binomial" + ) + ``` ## Description and filtering of the dataset @@ -490,6 +501,7 @@ ggplot(obs_pred_df, aes(x = model_name, y = RMSE)) + scale_y_continuous(trans="log10") + theme_bw() + facet_grid(Observation ~ .) + + scale_x_discrete(labels = model_name_labels) + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) ``` @@ -498,21 +510,29 @@ The fits of the negative binomial can be evaluated through plotting the estimate ``` {r Plot precision parameters for negative binomial models, fig.width = 6} -ggplot(obs_pred_df %>% - dplyr::filter(!is.na(phi)) %>% - dplyr::group_by(model_name) %>% - dplyr::slice(1) %>% - dplyr::ungroup(), - aes(x = model_name, - y = phi, - ymin = phi_lower, - ymax = phi_upper)) + - geom_point() + - geom_errorbar(width = 0.25) + - theme_bw() + - scale_y_continuous(trans="log10") + - ylab(expression(phi)) + - theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +(phi_plot <- + ggplot(obs_pred_df %>% + dplyr::filter(!is.na(phi)) %>% + dplyr::group_by(model_name) %>% + dplyr::slice(1) %>% + dplyr::ungroup(), + aes(x = model_name, + y = phi, + ymin = phi_lower, + ymax = phi_upper)) + + geom_point() + + geom_errorbar(width = 0.25) + + theme_bw() + + scale_y_continuous(trans="log10") + + ylab(expression(phi)) + + scale_x_discrete(labels = model_name_labels[c(2,4,6,8)]) + + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +) + +ggsave(phi_plot, + file="adult_serotype_phi_plot.pdf", + height = 6, + width = 6) ``` @@ -520,7 +540,7 @@ ggplot(obs_pred_df %>% As the models can instead be compared with Bayes factors: -``` {r Comparison with BF, include = FALSE} +``` {r Comparison with BF, include = TRUE} bf_comparison <- progressionEstimation::compare_model_fits_with_bf(fit_list, num_iter = n_iter, @@ -544,18 +564,18 @@ full_adult_serotype_invasiveness <- ) ) -full_adjusted_type_specific_poisson_fit <- +full_adjusted_type_specific_negbin_fit <- progressionEstimation::fit_progression_rate_model(full_adult_serotype_invasiveness, type_specific = TRUE, location_adjustment = TRUE, - stat_model = "poisson", + stat_model = "negbin", num_chains = n_chains, num_iter = n_iter, num_cores = n_core) -rhat_plot <- plot(full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005) +rhat_plot <- plot(full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005) -trace_plot <- rstan::traceplot(full_adjusted_type_specific_poisson_fit, pars = "lp__") + +trace_plot <- rstan::traceplot(full_adjusted_type_specific_negbin_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90)) (best_fitting_model_validation_plot <- @@ -579,7 +599,7 @@ mixedrank = function(x) order(gtools::mixedorder(as.character(x))) # Annotate serotypes by status best_fitting_output <- - progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_poisson_fit, + progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_negbin_fit, S_pneumoniae_adult_serotype) %>% dplyr::mutate("classification" = dplyr::case_when( type %in% vaccine_types[["PCV7"]] ~ "PCV7", @@ -640,6 +660,83 @@ write.csv(best_fitting_output %>% ``` +## Compare invasiveness values with those from children + +``` {r Comparison with infant values} + +infant_data <- read.csv("Dataset_S1.csv") %>% + dplyr::mutate("classification" = dplyr::case_when( + type %in% vaccine_types[["PCV7"]] ~ "PCV7", + type %in% vaccine_types[["PCV10"]] ~ "PCV10", + type %in% vaccine_types[["PCV13"]] ~ "PCV13", + type %in% vaccine_types[["PCV15"]] ~ "PCV15", + type %in% vaccine_types[["PCV20"]] ~ "PCV20", + type %in% vaccine_types[["PPV23"]] ~ "PPV23", + TRUE ~ "No PCV" + ) + ) %>% + dplyr::mutate(classification = factor(classification, levels = c("PCV7", + "PCV10", + "PCV13", + "PCV15", + "PCV20", + "PPV23", + "No PCV"))) + +joint_invasiveness <- + infant_data %>% + dplyr::rename(infant_nu = invasiveness) %>% + dplyr::rename(infant_nu_lower = invasiveness_lower) %>% + dplyr::rename(infant_nu_upper = invasiveness_upper) %>% + dplyr::left_join( + best_fitting_output %>% + dplyr::select(type,nu,nu_lower,nu_upper) %>% + dplyr::distinct(), + by = c("type") + ) %>% + dplyr::filter(!is.na(nu)) + +serotypes_to_label <- c("1","27","12F","12B","8","29","6C","18B","33A","10F","35A","11A") + +joint_invasiveness_plot <- + ggplot(joint_invasiveness, + aes( + x = nu, + y = infant_nu, + xmin = nu_lower, + xmax = nu_upper, + ymin = infant_nu_lower, + ymax = infant_nu_upper, + colour = classification + ) + ) + + geom_point() + + geom_errorbar(alpha = 0.5) + + geom_errorbarh(alpha = 0.5) + + scale_x_continuous(trans = "log10") + + scale_y_continuous(trans = "log10") + + scale_colour_manual(values = vaccine_colours) + + xlab("Progression rate estimate in adults (disease per carrier per year)") + + ylab("Progression rate estimate in infants (disease per carrier per year)") + + ggrepel::geom_label_repel(data = joint_invasiveness %>% + dplyr::filter(type %in% serotypes_to_label), + aes(label = type)) + + theme_bw() + + theme(legend.position = "none") + +overall_inv_analysis_plot <- + cowplot::plot_grid(plotlist = list(invasiveness_plot,joint_invasiveness_plot), + nrow = 2, + ncol = 1, + labels = "AUTO") + +ggsave(overall_inv_analysis_plot, + file = "joint_child_adult_invasiveness_plot.pdf", + height = 11, + width = 8) + +``` + ## Plot study-specific scale factors ``` {r Plot study-specific scale factor estimates from best-fitting model} @@ -647,6 +744,11 @@ write.csv(best_fitting_output %>% (scale_factor_plot <- progressionEstimation::plot_study_scale_factors(best_fitting_output)) +ggsave(scale_factor_plot, + file = "adult_serotype_scale_factor_plot.png", + width = 8, + height = 6) + ``` ## Compare a model fit that account for PCVs protecting against disease @@ -676,18 +778,18 @@ pv_S_pneumoniae_adult_serotype %<>% pv_full_adult_serotype_invasiveness <- progressionEstimation::process_input_data(pv_S_pneumoniae_adult_serotype) -pv_full_adjusted_type_specific_poisson_fit <- +pv_full_adjusted_type_specific_negbin_fit <- progressionEstimation::fit_progression_rate_model(pv_full_adult_serotype_invasiveness, type_specific = TRUE, location_adjustment = TRUE, - stat_model = "poisson", + stat_model = "negbin", num_chains = n_chains, num_iter = n_iter, num_cores = n_core) -rhat_plot <- plot(pv_full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005) +rhat_plot <- plot(pv_full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005) -trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_poisson_fit, pars = "lp__") +trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_negbin_fit, pars = "lp__") cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot), nrow = 1, @@ -699,7 +801,7 @@ cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot), pv_best_fitting_output <- progressionEstimation::process_progression_rate_model_output( - pv_full_adjusted_type_specific_poisson_fit, pv_S_pneumoniae_adult_serotype) %>% + pv_full_adjusted_type_specific_negbin_fit, pv_S_pneumoniae_adult_serotype) %>% dplyr::mutate("classification" = dplyr::case_when( gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7", gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10", @@ -900,9 +1002,9 @@ combined_invasiveness_df <- # Plot comparison of invasiveness estimates ggplot(combined_invasiveness_df, - aes(x = Invasiveness_adjusted_type_specific_poisson, - xmin = Invasiveness_lower_adjusted_type_specific_poisson, - xmax = Invasiveness_upper_adjusted_type_specific_poisson, + aes(x = Invasiveness_adjusted_type_specific_negbin, + xmin = Invasiveness_lower_adjusted_type_specific_negbin, + xmax = Invasiveness_upper_adjusted_type_specific_negbin, y = Invasiveness_FE, ymin = Invasiveness_lower_FE, ymax = Invasiveness_upper_FE, @@ -915,15 +1017,15 @@ ggplot(combined_invasiveness_df, scale_color_manual(values = vaccine_colours) + theme(legend.position = "bottom") + ylab("Invasiveness estimated from log odds ratio") + - xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") + + xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") + facet_wrap(~Sample_count) + - stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson, + stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin, y = Invasiveness_FE), inherit.aes = FALSE, method = "kendall", cor.coef.name = "tau") + ggrepel::geom_label_repel(data = combined_invasiveness_df %>% - dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), + dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), aes(label = Serotype) ) @@ -933,9 +1035,9 @@ ggplot(combined_invasiveness_df, # Plot comparison of invasiveness estimates ggplot(combined_invasiveness_df, - aes(x = Invasiveness_adjusted_type_specific_poisson, - xmin = Invasiveness_lower_adjusted_type_specific_poisson, - xmax = Invasiveness_upper_adjusted_type_specific_poisson, + aes(x = Invasiveness_adjusted_type_specific_negbin, + xmin = Invasiveness_lower_adjusted_type_specific_negbin, + xmax = Invasiveness_upper_adjusted_type_specific_negbin, y = Invasiveness_REML, ymin = Invasiveness_lower_REML, ymax = Invasiveness_upper_REML, @@ -948,15 +1050,15 @@ ggplot(combined_invasiveness_df, scale_color_manual(values = vaccine_colours) + theme(legend.position = "bottom") + ylab("Invasiveness estimated from log odds ratio") + - xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") + + xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") + facet_wrap(~Sample_count) + - stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson, + stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin, y = Invasiveness_REML), inherit.aes = FALSE, method = "kendall", cor.coef.name = "tau") + ggrepel::geom_label_repel(data = combined_invasiveness_df %>% - dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), + dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), aes(label = Serotype) ) diff --git a/examples/s-pneumoniae-serotype-invasiveness-adults.html b/examples/s-pneumoniae-serotype-invasiveness-adults.html index 2993ad0..d228813 100644 --- a/examples/s-pneumoniae-serotype-invasiveness-adults.html +++ b/examples/s-pneumoniae-serotype-invasiveness-adults.html @@ -14,230 +14,9 @@ s-pneumoniae-serotype-invasiveness-adults - - + + + + @@ -542,98 +143,100 @@

s-pneumoniae-serotype-invasiveness-adults

-
# Load dependencies
-require(tidyverse)
-#> Loading required package: tidyverse
-#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
-#> ✓ ggplot2 3.3.5     ✓ purrr   0.3.4
-#> ✓ tibble  3.1.3     ✓ dplyr   1.0.7
-#> ✓ tidyr   1.1.3     ✓ stringr 1.4.0
-#> ✓ readr   1.4.0     ✓ forcats 0.5.1
-#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
-#> x dplyr::filter() masks stats::filter()
-#> x dplyr::lag()    masks stats::lag()
-require(magrittr)
-#> Loading required package: magrittr
-#> 
-#> Attaching package: 'magrittr'
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-#> 
-#>     set_names
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-#> 
-#>     extract
-require(rstan)
-#> Loading required package: rstan
-#> Loading required package: StanHeaders
-#> rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
-#> For execution on a local, multicore CPU with excess RAM we recommend calling
-#> options(mc.cores = parallel::detectCores()).
-#> To avoid recompilation of unchanged Stan programs, we recommend calling
-#> rstan_options(auto_write = TRUE)
-#> 
-#> Attaching package: 'rstan'
-#> The following object is masked from 'package:magrittr':
-#> 
-#>     extract
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-#> 
-#>     extract
-require(bridgesampling)
-#> Loading required package: bridgesampling
-require(loo)
-#> Loading required package: loo
-#> This is loo version 2.4.1
-#> - Online documentation and vignettes at mc-stan.org/loo
-#> - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
-#> 
-#> Attaching package: 'loo'
-#> The following object is masked from 'package:rstan':
-#> 
-#>     loo
-require(cowplot)
-#> Loading required package: cowplot
-require(ggrepel)
-#> Loading required package: ggrepel
-require(xlsx)
-#> Loading required package: xlsx
-
-# Load stan package
-library(progressionEstimation)
-pkgbuild::compile_dll()
-roxygen2::roxygenize(package.dir = "..")
-#> ℹ Loading progressionEstimation
-#> Loading required package: kableExtra
-#> 
-#> Attaching package: 'kableExtra'
-#> The following object is masked from 'package:dplyr':
-#> 
-#>     group_rows
-#> Writing NAMESPACE
-#> Writing NAMESPACE
-
-# Define serotype categories and palettes
-vaccine_types <- list(
-  "PCV7" = c("4","6B","9V","14","18C","19F","23F"),
-  "PCV10" = c("1","5","7F"),
-  "PCV13" = c("6A","3","19A"),
-  "PCV15" = c("22F","33F"),
-  "PCV20" = c("8","10A","11A","12F","15B/C"),
-  "PPV23" = c("2","9N","17F","20")
-)
-
-vaccine_colours <- c("No PCV" = "blue",
-                     "PCV7" = "red",
-                     "PCV10" = "orange",
-                     "PCV13" = "coral2",
-                     "PCV15" = "pink",
-                     "PCV20" = "purple",
-                     "PPV23" = "black")
-
-epi_colors <- c(
-  "carriage" = "skyblue",
-  "disease" = "cornflowerblue"
-)
+
# Load dependencies
+require(tidyverse)
+#> Loading required package: tidyverse
+#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
+#> ✓ ggplot2 3.3.5     ✓ purrr   0.3.4
+#> ✓ tibble  3.1.6     ✓ dplyr   1.0.7
+#> ✓ tidyr   1.1.4     ✓ stringr 1.4.0
+#> ✓ readr   2.1.0     ✓ forcats 0.5.1
+#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
+#> x dplyr::filter() masks stats::filter()
+#> x dplyr::lag()    masks stats::lag()
+require(magrittr)
+#> Loading required package: magrittr
+#> 
+#> Attaching package: 'magrittr'
+#> The following object is masked from 'package:purrr':
+#> 
+#>     set_names
+#> The following object is masked from 'package:tidyr':
+#> 
+#>     extract
+require(rstan)
+#> Loading required package: rstan
+#> Loading required package: StanHeaders
+#> rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
+#> For execution on a local, multicore CPU with excess RAM we recommend calling
+#> options(mc.cores = parallel::detectCores()).
+#> To avoid recompilation of unchanged Stan programs, we recommend calling
+#> rstan_options(auto_write = TRUE)
+#> 
+#> Attaching package: 'rstan'
+#> The following object is masked from 'package:magrittr':
+#> 
+#>     extract
+#> The following object is masked from 'package:tidyr':
+#> 
+#>     extract
+require(bridgesampling)
+#> Loading required package: bridgesampling
+require(loo)
+#> Loading required package: loo
+#> This is loo version 2.4.1
+#> - Online documentation and vignettes at mc-stan.org/loo
+#> - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
+#> 
+#> Attaching package: 'loo'
+#> The following object is masked from 'package:rstan':
+#> 
+#>     loo
+require(cowplot)
+#> Loading required package: cowplot
+require(ggrepel)
+#> Loading required package: ggrepel
+require(xlsx)
+#> Loading required package: xlsx
+
+# Load stan package
+library(progressionEstimation)
+#pkgbuild::compile_dll()
+#roxygen2::roxygenize(package.dir = "..")
+
+# Define serotype categories and palettes
+vaccine_types <- list(
+  "PCV7" = c("4","6B","9V","14","18C","19F","23F"),
+  "PCV10" = c("1","5","7F"),
+  "PCV13" = c("6A","3","19A"),
+  "PCV15" = c("22F","33F"),
+  "PCV20" = c("8","10A","11A","12F","15B/C"),
+  "PPV23" = c("2","9N","17F","20")
+)
+
+vaccine_colours <- c("No PCV" = "blue",
+                     "PCV7" = "red",
+                     "PCV10" = "orange",
+                     "PCV13" = "coral2",
+                     "PCV15" = "pink",
+                     "PCV20" = "purple",
+                     "PPV23" = "black")
+
+epi_colors <- c(
+  "carriage" = "skyblue",
+  "disease" = "cornflowerblue"
+)
+
+model_name_labels <-
+  c("null Poisson",
+    "null negative binomial",
+    "type-specific Poisson",
+    "type-specific negative binomial",
+    "study-adjusted Poisson",
+    "study-adjusted negative binomial",
+    "study-adjusted type-specific Poisson",
+    "study-adjusted type-specific negative binomial"
+  )

Description and filtering of the dataset

The dataset used in this analysis is contained in the S_pneumoniae_adult_serotype object, which includes data from 5 studies on 53 serotypes. The distribution of samples between each study can be plotted, if they are ranked by the mean number of carriage and disease isolates:

@@ -660,604 +263,777 @@

Fitting the statistical models

This can also be used with the negative binomial model (adjusted type-specific negative binomial model):

\[d_{i,j} \sim NegBin(\delta_{i}\nu_{j}\rho_{i,j}N_{i}t_{i},\phi)\]

To check the models have fitted correctly, we can plot the \(\hat{R}\) values across MCMCs:

-

-fit_list <- list(null_poisson_fit,
-                 null_negbin_fit,
-                 type_specific_poisson_fit,
-                 type_specific_negbin_fit,
-                 adjusted_poisson_fit,
-                 adjusted_negbin_fit,
-                 adjusted_type_specific_poisson_fit,
-                 adjusted_type_specific_negbin_fit)
-
-
-plot_rhat <- function(fit) {
-  rhat_plot <- plot(fit, plotfun = "rhat", binwidth = 0.00005) +
-                theme(axis.text.x = element_text(angle = 90))
-  return(rhat_plot)
-}
-
-rhat_plots <- lapply(fit_list, plot_rhat)
-
-combined_rhat_plots <- cowplot::plot_grid(plotlist = rhat_plots, ncol = 4, nrow = 2, labels = "AUTO")
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-ggsave(combined_rhat_plots,
-       file = "adult_combined_rhat_plots.png",
-       width = 8,
-       height = 6)
+

+fit_list <- list(null_poisson_fit,
+                 null_negbin_fit,
+                 type_specific_poisson_fit,
+                 type_specific_negbin_fit,
+                 adjusted_poisson_fit,
+                 adjusted_negbin_fit,
+                 adjusted_type_specific_poisson_fit,
+                 adjusted_type_specific_negbin_fit)
+
+
+plot_rhat <- function(fit) {
+  rhat_plot <- plot(fit, plotfun = "rhat", binwidth = 0.00005) +
+                theme(axis.text.x = element_text(angle = 90))
+  return(rhat_plot)
+}
+
+rhat_plots <- lapply(fit_list, plot_rhat)
+
+combined_rhat_plots <- cowplot::plot_grid(plotlist = rhat_plots, ncol = 4, nrow = 2, labels = "AUTO")
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+ggsave(combined_rhat_plots,
+       file = "adult_combined_rhat_plots.png",
+       width = 8,
+       height = 6)

Convergence can also be checked using trace plots of the log likelihood values:

-

-plot_lp <- function(fit) {
-  pl <- rstan::traceplot(fit, pars = "lp__")
-  no_leg_pl <- pl + theme(legend.position = "none",
-                          axis.text.x = element_text(angle = 90))
-  return(no_leg_pl)
-}
-
-trace_plots <- lapply(fit_list, plot_lp)
-
-combined_trace_plots <- 
-  cowplot::plot_grid(plotlist = trace_plots, ncol = 4, nrow = 2, labels = "AUTO")
-
-ggsave(combined_trace_plots,
-       file = "adult_combined_trace_plots.png",
-       width = 8,
-       height = 6)
+

+plot_lp <- function(fit) {
+  pl <- rstan::traceplot(fit, pars = "lp__")
+  no_leg_pl <- pl + theme(legend.position = "none",
+                          axis.text.x = element_text(angle = 90))
+  return(no_leg_pl)
+}
+
+trace_plots <- lapply(fit_list, plot_lp)
+
+combined_trace_plots <- 
+  cowplot::plot_grid(plotlist = trace_plots, ncol = 4, nrow = 2, labels = "AUTO")
+
+ggsave(combined_trace_plots,
+       file = "adult_combined_trace_plots.png",
+       width = 8,
+       height = 6)

Compare model observations and predictions

For each model, the output can be processed, and the observations plotted against each model’s predictions.

-

-model_outputs <- lapply(fit_list,
-                        progressionEstimation::process_progression_rate_model_output,
-                        filtered_S_pneumoniae_adult_serotype)
-
-prediction_plots <- lapply(model_outputs,
-                           progressionEstimation::plot_case_carrier_predictions,
-                           legend = FALSE,
-                           n_label = 0)
-
-no_leg_plot <- cowplot::plot_grid(plotlist = prediction_plots,
-                                  ncol = 1,
-                                  nrow = 8,
-                                  labels = "AUTO",
-                                  vjust = -0.01) +
-      theme(plot.margin = unit(c(0.5,0,0,0), "cm"))
-
-prediction_plot_legend <- progressionEstimation::plot_case_carrier_predictions(model_outputs[[1]], just_legend = TRUE)
-
-pred_v_obs_plot <- 
-  cowplot::plot_grid(no_leg_plot,
-                     prediction_plot_legend,
-                     ncol = 1,
-                     rel_heights = c(1,0.1))
-
-ggsave(pred_v_obs_plot,
-       file = "adult_serotypes_pred_v_obs_plot.png",
-       height = 20,
-       width = 10)
+

+model_outputs <- lapply(fit_list,
+                        progressionEstimation::process_progression_rate_model_output,
+                        filtered_S_pneumoniae_adult_serotype)
+
+prediction_plots <- lapply(model_outputs,
+                           progressionEstimation::plot_case_carrier_predictions,
+                           legend = FALSE,
+                           n_label = 0)
+
+no_leg_plot <- cowplot::plot_grid(plotlist = prediction_plots,
+                                  ncol = 1,
+                                  nrow = 8,
+                                  labels = "AUTO",
+                                  vjust = -0.01) +
+      theme(plot.margin = unit(c(0.5,0,0,0), "cm"))
+
+prediction_plot_legend <- progressionEstimation::plot_case_carrier_predictions(model_outputs[[1]], just_legend = TRUE)
+
+pred_v_obs_plot <- 
+  cowplot::plot_grid(no_leg_plot,
+                     prediction_plot_legend,
+                     ncol = 1,
+                     rel_heights = c(1,0.1))
+
+ggsave(pred_v_obs_plot,
+       file = "adult_serotypes_pred_v_obs_plot.png",
+       height = 20,
+       width = 10)

The deviation of the predicted and observed values can be simply evaluated using the root mean square error:

-

-obs_pred_df <-
-  dplyr::bind_rows(model_outputs) %>%
-  dplyr::select(model_name,carriage_rmse,disease_rmse,phi,phi_lower,phi_upper) %>%
-  tidyr::pivot_longer(c(carriage_rmse,disease_rmse), names_to = "Observation", values_to = "RMSE") %>%
-  dplyr::mutate(model_name = factor(model_name,
-                                    levels = c(
-                                      "null_poisson",
-                                      "null_negbin",
-                                      "type_specific_poisson",
-                                      "type_specific_negbin",
-                                      "adjusted_null_poisson",
-                                      "adjusted_null_negbin",
-                                      "adjusted_type_specific_poisson",
-                                      "adjusted_type_specific_negbin"
-                                      )
-                                    )
-                ) %>%
-  dplyr::mutate(Observation = dplyr::case_when(
-                    Observation == "carriage_rmse" ~ "Carriage",
-                    Observation == "disease_rmse" ~ "Disease"
-                  )
-                )
-
-ggplot(obs_pred_df, aes(x = model_name, y = RMSE)) +
-  #geom_boxplot(outlier.shape = NA) +
-  geom_point(position = position_jitter(width = 0.25),
-             alpha = 0.25,
-             cex = 0.75,
-             colour = "blue",
-             pch = 4) +
-  geom_violin(fill = NA) +
-  scale_y_continuous(trans="log10") +
-  theme_bw() +
-  facet_grid(Observation ~ .) +
-  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
-

+

+obs_pred_df <-
+  dplyr::bind_rows(model_outputs) %>%
+  dplyr::select(model_name,carriage_rmse,disease_rmse,phi,phi_lower,phi_upper) %>%
+  tidyr::pivot_longer(c(carriage_rmse,disease_rmse), names_to = "Observation", values_to = "RMSE") %>%
+  dplyr::mutate(model_name = factor(model_name,
+                                    levels = c(
+                                      "null_poisson",
+                                      "null_negbin",
+                                      "type_specific_poisson",
+                                      "type_specific_negbin",
+                                      "adjusted_null_poisson",
+                                      "adjusted_null_negbin",
+                                      "adjusted_type_specific_poisson",
+                                      "adjusted_type_specific_negbin"
+                                      )
+                                    )
+                ) %>%
+  dplyr::mutate(Observation = dplyr::case_when(
+                    Observation == "carriage_rmse" ~ "Carriage",
+                    Observation == "disease_rmse" ~ "Disease"
+                  )
+                )
+
+ggplot(obs_pred_df, aes(x = model_name, y = RMSE)) +
+  #geom_boxplot(outlier.shape = NA) +
+  geom_point(position = position_jitter(width = 0.25),
+             alpha = 0.25,
+             cex = 0.75,
+             colour = "blue",
+             pch = 4) +
+  geom_violin(fill = NA) +
+  scale_y_continuous(trans="log10") +
+  theme_bw() +
+  facet_grid(Observation ~ .) +
+  scale_x_discrete(labels = model_name_labels) +
+  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+

The fits of the negative binomial can be evaluated through plotting the estimates of the precision parameter, \(\phi\). As \(\phi\) increases, the variance of the negative binomial distribution decreases, and the negative binomal model becomes more similar to the Poisson model.

-

-ggplot(obs_pred_df %>%
-        dplyr::filter(!is.na(phi)) %>%
-        dplyr::group_by(model_name) %>%
-        dplyr::slice(1) %>%
-        dplyr::ungroup(),
-      aes(x = model_name,
-          y = phi,
-          ymin = phi_lower,
-          ymax = phi_upper)) +
-  geom_point() +
-  geom_errorbar(width = 0.25) +
-  theme_bw() +
-  scale_y_continuous(trans="log10") +
-  ylab(expression(phi)) +
-  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
-

+

+(phi_plot <-
+  ggplot(obs_pred_df %>%
+          dplyr::filter(!is.na(phi)) %>%
+          dplyr::group_by(model_name) %>%
+          dplyr::slice(1) %>%
+          dplyr::ungroup(),
+        aes(x = model_name,
+            y = phi,
+            ymin = phi_lower,
+            ymax = phi_upper)) +
+    geom_point() +
+    geom_errorbar(width = 0.25) +
+    theme_bw() +
+    scale_y_continuous(trans="log10") +
+    ylab(expression(phi)) +
+    scale_x_discrete(labels = model_name_labels[c(2,4,6,8)]) +
+    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+)
+

+

+ggsave(phi_plot,
+       file="adult_serotype_phi_plot.pdf",
+       height = 6,
+       width = 6)

Run model comparison with Bayes factors

As the models can instead be compared with Bayes factors:

+

+bf_comparison <- progressionEstimation::compare_model_fits_with_bf(fit_list,
+                                                                   num_iter = n_iter,
+                                                                   num_threads = n_core)
+bf_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Model + +log_Bayes_factor +
+adjusted_type_specific_negbin + +0.00000 +
+adjusted_type_specific_poisson + +-16.98297 +
+adjusted_null_negbin + +-17.46109 +
+null_negbin + +-28.34090 +
+type_specific_negbin + +-36.34326 +
+type_specific_poisson + +-470.77830 +
+adjusted_null_poisson + +-945.85092 +
+null_poisson + +-1814.04519 +

Plot serotype invasiveness

The best-fitting model can then be applied to the overall dataset.

-

-full_adult_serotype_invasiveness <- 
-  progressionEstimation::process_input_data(
-    S_pneumoniae_adult_serotype %<>%
-      dplyr::mutate(study = factor(study, levels = studies_by_size)
-      )
-    )
-
-full_adjusted_type_specific_poisson_fit <- 
-  progressionEstimation::fit_progression_rate_model(full_adult_serotype_invasiveness,
-                                                    type_specific = TRUE,
-                                                    location_adjustment = TRUE,
-                                                    stat_model = "poisson",
-                                                    num_chains = n_chains,
-                                                    num_iter = n_iter,
-                                                    num_cores = n_core)
-
-rhat_plot <- plot(full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005)
-
-trace_plot <- rstan::traceplot(full_adjusted_type_specific_poisson_fit, pars = "lp__") +
-                theme(axis.text.x = element_text(angle = 90))
-
-(best_fitting_model_validation_plot <-
-  cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
-                     nrow = 1,
-                     ncol = 2,
-                     labels = "AUTO")
-)
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-

-

-ggsave(best_fitting_model_validation_plot,
-       file = "best_fitting_adult_model_validation_plot.png",
-       width = 8,
-       height = 6)
-

-mixedrank = function(x) order(gtools::mixedorder(as.character(x)))
-
-# Annotate serotypes by status
-best_fitting_output <- 
-  progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_poisson_fit,
-                                                               S_pneumoniae_adult_serotype) %>%
-    dplyr::mutate("classification" = dplyr::case_when(
-        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
-        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
-        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
-        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
-        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
-        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
-        TRUE ~ "No PCV"
-      )
-    ) %>%
-    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
-                                                                     "PCV10",
-                                                                     "PCV13",
-                                                                     "PCV15",
-                                                                     "PCV20",
-                                                                     "PPV23",
-                                                                     "No PCV")))
-
-# Order serotypes
-serotype_levels <-
-  best_fitting_output %>%
-    dplyr::select(type,classification) %>%
-    dplyr::distinct() %>%
-    group_by(classification) %>%
-    dplyr::arrange(mixedrank(type),
-                   .by_group = TRUE) %>%
-    ungroup() %>%
-    dplyr::select(type) %>%
-    dplyr::pull()
-
-best_fitting_output %<>%
-  dplyr::mutate(type = factor(type, levels = serotype_levels))
-
-# Plot
-(invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(best_fitting_output,
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE))
-

-

-ggsave(invasiveness_plot,
-       file = "full_serotype_invasiveness_plot.png",
-       height = 8,
-       width = 8)
-
-write.csv(best_fitting_output %>%
-            dplyr::select(type,nu,nu_lower,nu_upper) %>%
-            dplyr::rename(invasiveness = nu) %>%
-            dplyr::rename(invasiveness_lower = nu_lower) %>%
-            dplyr::rename(invasiveness_upper = nu_upper) %>%
-            dplyr::distinct(),
-          file = "Dataset_S2.csv",
-          quote = F,
-          row.names = F)
+

+full_adult_serotype_invasiveness <- 
+  progressionEstimation::process_input_data(
+    S_pneumoniae_adult_serotype %<>%
+      dplyr::mutate(study = factor(study, levels = studies_by_size)
+      )
+    )
+
+full_adjusted_type_specific_negbin_fit <- 
+  progressionEstimation::fit_progression_rate_model(full_adult_serotype_invasiveness,
+                                                    type_specific = TRUE,
+                                                    location_adjustment = TRUE,
+                                                    stat_model = "negbin",
+                                                    num_chains = n_chains,
+                                                    num_iter = n_iter,
+                                                    num_cores = n_core)
+
+rhat_plot <- plot(full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005)
+
+trace_plot <- rstan::traceplot(full_adjusted_type_specific_negbin_fit, pars = "lp__") +
+                theme(axis.text.x = element_text(angle = 90))
+
+(best_fitting_model_validation_plot <-
+  cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
+                     nrow = 1,
+                     ncol = 2,
+                     labels = "AUTO")
+)
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+

+

+ggsave(best_fitting_model_validation_plot,
+       file = "best_fitting_adult_model_validation_plot.png",
+       width = 8,
+       height = 6)
+

+mixedrank = function(x) order(gtools::mixedorder(as.character(x)))
+
+# Annotate serotypes by status
+best_fitting_output <- 
+  progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_negbin_fit,
+                                                               S_pneumoniae_adult_serotype) %>%
+    dplyr::mutate("classification" = dplyr::case_when(
+        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
+        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
+        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
+        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
+        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
+        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
+        TRUE ~ "No PCV"
+      )
+    ) %>%
+    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                     "PCV10",
+                                                                     "PCV13",
+                                                                     "PCV15",
+                                                                     "PCV20",
+                                                                     "PPV23",
+                                                                     "No PCV")))
+
+# Order serotypes
+serotype_levels <-
+  best_fitting_output %>%
+    dplyr::select(type,classification) %>%
+    dplyr::distinct() %>%
+    group_by(classification) %>%
+    dplyr::arrange(mixedrank(type),
+                   .by_group = TRUE) %>%
+    ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::pull()
+
+best_fitting_output %<>%
+  dplyr::mutate(type = factor(type, levels = serotype_levels))
+
+# Plot
+(invasiveness_plot <-
+  progressionEstimation::plot_progression_rates(best_fitting_output,
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE))
+

+

+ggsave(invasiveness_plot,
+       file = "full_serotype_invasiveness_plot.png",
+       height = 8,
+       width = 8)
+
+write.csv(best_fitting_output %>%
+            dplyr::select(type,nu,nu_lower,nu_upper) %>%
+            dplyr::rename(invasiveness = nu) %>%
+            dplyr::rename(invasiveness_lower = nu_lower) %>%
+            dplyr::rename(invasiveness_upper = nu_upper) %>%
+            dplyr::distinct(),
+          file = "Dataset_S2.csv",
+          quote = F,
+          row.names = F)
+
+
+

Compare invasiveness values with those from children

+

+infant_data <- read.csv("Dataset_S1.csv") %>%
+    dplyr::mutate("classification" = dplyr::case_when(
+        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
+        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
+        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
+        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
+        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
+        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
+        TRUE ~ "No PCV"
+      )
+    ) %>%
+    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                     "PCV10",
+                                                                     "PCV13",
+                                                                     "PCV15",
+                                                                     "PCV20",
+                                                                     "PPV23",
+                                                                     "No PCV")))
+
+joint_invasiveness <-
+  infant_data %>%
+    dplyr::rename(infant_nu = invasiveness) %>%
+    dplyr::rename(infant_nu_lower = invasiveness_lower) %>%
+    dplyr::rename(infant_nu_upper = invasiveness_upper) %>%
+    dplyr::left_join(
+      best_fitting_output %>%
+          dplyr::select(type,nu,nu_lower,nu_upper) %>%
+          dplyr::distinct(),
+      by = c("type")
+    ) %>%
+    dplyr::filter(!is.na(nu))
+
+serotypes_to_label <- c("1","27","12F","12B","8","29","6C","18B","33A","10F","35A","11A")
+
+joint_invasiveness_plot <-
+  ggplot(joint_invasiveness,
+         aes(
+           x = nu,
+           y = infant_nu,
+           xmin = nu_lower,
+           xmax = nu_upper,
+           ymin = infant_nu_lower,
+           ymax = infant_nu_upper,
+           colour = classification
+          )
+         ) +
+    geom_point() +
+    geom_errorbar(alpha = 0.5) +
+    geom_errorbarh(alpha = 0.5) +
+    scale_x_continuous(trans = "log10") +
+    scale_y_continuous(trans = "log10") +
+    scale_colour_manual(values = vaccine_colours) +
+    xlab("Progression rate estimate in adults (disease per carrier per year)") +
+    ylab("Progression rate estimate in infants (disease per carrier per year)") +
+    ggrepel::geom_label_repel(data = joint_invasiveness %>%
+                                      dplyr::filter(type %in% serotypes_to_label),
+                              aes(label = type)) +
+    theme_bw() +
+    theme(legend.position = "none")
+
+overall_inv_analysis_plot <-
+  cowplot::plot_grid(plotlist = list(invasiveness_plot,joint_invasiveness_plot),
+                     nrow = 2,
+                     ncol = 1,
+                     labels = "AUTO")
+
+ggsave(overall_inv_analysis_plot,
+       file = "joint_child_adult_invasiveness_plot.pdf",
+       height = 11,
+       width = 8)

Plot study-specific scale factors

-

-(scale_factor_plot <-
-  progressionEstimation::plot_study_scale_factors(best_fitting_output))
-

+

+(scale_factor_plot <-
+  progressionEstimation::plot_study_scale_factors(best_fitting_output))
+

+

+ggsave(scale_factor_plot,
+       file = "adult_serotype_scale_factor_plot.png",
+       width = 8,
+       height = 6)

Compare a model fit that account for PCVs protecting against disease

If PCVs provide further protection against disease, relative to carriage, then their invasiveness may reduce post-PCV. Therefore we can treat them as different serotypes pre- and post-PCV.

-

-pv_S_pneumoniae_adult_serotype <-
-  S_pneumoniae_adult_serotype %>%
-    dplyr::mutate(type = dplyr::case_when(
-                      type %in% vaccine_types[["PCV7"]] & grepl("post.PCV", study) ~ paste0(type,"_pv"),
-                      type == "6A" & grepl("post.PCV", study) ~ paste0(type,"_pv"),
-                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV10", study) ~ paste0(type,"_pv"),
-                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
-                      type %in% vaccine_types[["PCV13"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
-                      type == "6C" & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
-                      TRUE ~ as.character(type)
-                    )
-                  ) %>%
-  dplyr::mutate(type = factor(type))
-
-pv_S_pneumoniae_adult_serotype %<>%
-  dplyr::mutate(study = factor(study, levels = studies_by_size))
-
-pv_full_adult_serotype_invasiveness <- 
-  progressionEstimation::process_input_data(pv_S_pneumoniae_adult_serotype)
-
-pv_full_adjusted_type_specific_poisson_fit <- 
-  progressionEstimation::fit_progression_rate_model(pv_full_adult_serotype_invasiveness,
-                                                    type_specific = TRUE,
-                                                    location_adjustment = TRUE,
-                                                    stat_model = "poisson",
-                                                    num_chains = n_chains,
-                                                    num_iter = n_iter,
-                                                    num_cores = n_core)
-
-rhat_plot <- plot(pv_full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005)
-
-trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_poisson_fit, pars = "lp__")
-
-cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
-                   nrow = 1,
-                   ncol = 2,
-                   labels = "AUTO")
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-

-

-pv_best_fitting_output <- 
-  progressionEstimation::process_progression_rate_model_output(
-    pv_full_adjusted_type_specific_poisson_fit,                                                 pv_S_pneumoniae_adult_serotype) %>%
-      dplyr::mutate("classification" = dplyr::case_when(
-          gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7",
-          gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10",
-          gsub("_pv","",type) %in% vaccine_types[["PCV13"]] ~ "PCV13",
-          gsub("_pv","",type) %in% vaccine_types[["PCV15"]] ~ "PCV15",
-          gsub("_pv","",type) %in% vaccine_types[["PCV20"]] ~ "PCV20",
-          gsub("_pv","",type) %in% vaccine_types[["PPV23"]] ~ "PPV23",
-          TRUE ~ "No PCV"
-        )
-      ) %>%
-      dplyr::mutate(classification = factor(classification, levels = c("PCV7",
-                                                                       "PCV10",
-                                                                       "PCV13",
-                                                                       "PCV15",
-                                                                       "PCV20",
-                                                                       "PPV23",
-                                                                       "No PCV")))
-
-# Order serotypes
-pv_serotype_levels <-
-  pv_best_fitting_output %>%
-    dplyr::select(type,classification) %>%
-    dplyr::distinct() %>%
-    group_by(classification) %>%
-    dplyr::arrange(mixedrank(type),
-                   .by_group = TRUE) %>%
-    ungroup() %>%
-    dplyr::select(type) %>%
-    dplyr::pull()
-
-pv_best_fitting_output %<>%
-  dplyr::mutate(type = factor(type, levels = pv_serotype_levels))
-
-# Plot
-(pv_invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(pv_best_fitting_output,
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE))
-

-

-(joint_invasiveness_plot <-
-    cowplot::plot_grid(plotlist = list(invasiveness_plot, pv_invasiveness_plot),
-                       nrow = 2,
-                       ncol = 1,
-                       labels = "AUTO"
-                       )
-)
+

+pv_S_pneumoniae_adult_serotype <-
+  S_pneumoniae_adult_serotype %>%
+    dplyr::mutate(type = dplyr::case_when(
+                      type %in% vaccine_types[["PCV7"]] & grepl("post.PCV", study) ~ paste0(type,"_pv"),
+                      type == "6A" & grepl("post.PCV", study) ~ paste0(type,"_pv"),
+                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV10", study) ~ paste0(type,"_pv"),
+                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
+                      type %in% vaccine_types[["PCV13"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
+                      type == "6C" & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
+                      TRUE ~ as.character(type)
+                    )
+                  ) %>%
+  dplyr::mutate(type = factor(type))
+
+pv_S_pneumoniae_adult_serotype %<>%
+  dplyr::mutate(study = factor(study, levels = studies_by_size))
+
+pv_full_adult_serotype_invasiveness <- 
+  progressionEstimation::process_input_data(pv_S_pneumoniae_adult_serotype)
+
+pv_full_adjusted_type_specific_negbin_fit <- 
+  progressionEstimation::fit_progression_rate_model(pv_full_adult_serotype_invasiveness,
+                                                    type_specific = TRUE,
+                                                    location_adjustment = TRUE,
+                                                    stat_model = "negbin",
+                                                    num_chains = n_chains,
+                                                    num_iter = n_iter,
+                                                    num_cores = n_core)
+
+rhat_plot <- plot(pv_full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005)
+
+trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_negbin_fit, pars = "lp__")
+
+cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
+                   nrow = 1,
+                   ncol = 2,
+                   labels = "AUTO")
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+

+

+pv_best_fitting_output <- 
+  progressionEstimation::process_progression_rate_model_output(
+    pv_full_adjusted_type_specific_negbin_fit,                                                 pv_S_pneumoniae_adult_serotype) %>%
+      dplyr::mutate("classification" = dplyr::case_when(
+          gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7",
+          gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10",
+          gsub("_pv","",type) %in% vaccine_types[["PCV13"]] ~ "PCV13",
+          gsub("_pv","",type) %in% vaccine_types[["PCV15"]] ~ "PCV15",
+          gsub("_pv","",type) %in% vaccine_types[["PCV20"]] ~ "PCV20",
+          gsub("_pv","",type) %in% vaccine_types[["PPV23"]] ~ "PPV23",
+          TRUE ~ "No PCV"
+        )
+      ) %>%
+      dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                       "PCV10",
+                                                                       "PCV13",
+                                                                       "PCV15",
+                                                                       "PCV20",
+                                                                       "PPV23",
+                                                                       "No PCV")))
+
+# Order serotypes
+pv_serotype_levels <-
+  pv_best_fitting_output %>%
+    dplyr::select(type,classification) %>%
+    dplyr::distinct() %>%
+    group_by(classification) %>%
+    dplyr::arrange(mixedrank(type),
+                   .by_group = TRUE) %>%
+    ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::pull()
+
+pv_best_fitting_output %<>%
+  dplyr::mutate(type = factor(type, levels = pv_serotype_levels))
+
+# Plot
+(pv_invasiveness_plot <-
+  progressionEstimation::plot_progression_rates(pv_best_fitting_output,
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE))
+

+

+(joint_invasiveness_plot <-
+    cowplot::plot_grid(plotlist = list(invasiveness_plot, pv_invasiveness_plot),
+                       nrow = 2,
+                       ncol = 1,
+                       labels = "AUTO"
+                       )
+)

-

-ggsave(joint_invasiveness_plot,
-       file = "join_adult_serotype_plot.png",
-       height = 10,
-       width = 8)
-

-(pv_scale_factor_plot <-
-  progressionEstimation::plot_study_scale_factors(pv_best_fitting_output))
-

+

+ggsave(joint_invasiveness_plot,
+       file = "join_adult_serotype_plot.png",
+       height = 10,
+       width = 8)
+

+(pv_scale_factor_plot <-
+  progressionEstimation::plot_study_scale_factors(pv_best_fitting_output))
+

Comparison with odds ratio calculation

-

-require(ggpubr)
-#> Loading required package: ggpubr
-#> 
-#> Attaching package: 'ggpubr'
-#> The following object is masked from 'package:cowplot':
-#> 
-#>     get_legend
-require(metafor)
-#> Loading required package: metafor
-#> Loading required package: Matrix
-#> 
-#> Attaching package: 'Matrix'
-#> The following objects are masked from 'package:tidyr':
-#> 
-#>     expand, pack, unpack
-#> 
-#> Loading the 'metafor' package (version 3.0-2). For an
-#> introduction to the package please type: help(metafor)
-
-get_serotype_stats <- function(serotype, df) {
-  sero_df <-
-    df %>%
-      tidyr::pivot_longer(c(carriage,disease),
-                          names_to = "clinical_manifestation",
-                          values_to = "observation") %>%
-      dplyr::group_by(study) %>%
-      dplyr::mutate(matching_type = dplyr::if_else(type == serotype,1,0)) %>%
-      dplyr::mutate(matching_type_disease =
-                      sum(observation[clinical_manifestation == "disease" & matching_type == 1])) %>%
-      dplyr::mutate(matching_type_carriage =
-                      sum(observation[clinical_manifestation == "carriage" & matching_type == 1])) %>%
-      dplyr::mutate(non_matching_type_disease =
-                      sum(observation[clinical_manifestation == "disease" & matching_type == 0])) %>%
-      dplyr::mutate(non_matching_type_carriage =
-                      sum(observation[clinical_manifestation == "carriage" & matching_type == 0])) %>%
-      dplyr::ungroup() %>%
-    dplyr::select(study,matching_type_disease,matching_type_carriage,non_matching_type_disease,non_matching_type_carriage) %>%
-    dplyr::distinct() %>%
-    dplyr::mutate(serotype = serotype) %>%
-    dplyr::filter(matching_type_carriage > 0 | matching_type_disease > 0)
-  return(sero_df)
-}
-
-per_serotype_estimate <- function(test_serotype, df, method_type = "FE") {
-  per_serotype_out <- metafor::rma(yi = yi,
-                                   vi = vi,
-                                   data = df,
-                                   slab = study,
-                                   subset = serotype == test_serotype,
-                                   method = method_type,
-                                   control=list(stepadj=0.5, maxiter=10000))
-  summary_df <-
-    data.frame(
-      "Analysis" = method_type,
-      "Serotype" = test_serotype,
-      "OR" = as.numeric(per_serotype_out$b),
-      "OR_upper" = per_serotype_out$ci.ub,
-      "OR_lower" = per_serotype_out$ci.lb,
-      "tau_squared" = per_serotype_out$tau2,
-      "i_squared" = per_serotype_out$I2,
-      "h_squared" = per_serotype_out$H2
-    )
-  return(summary_df)
-}
-
-serotype_or_df <- dplyr::bind_rows(lapply(
-                                   serotype_levels,
-                                   get_serotype_stats,
-                                   S_pneumoniae_adult_serotype)
-)
-
-serotype_effect_size_df <- metafor::escalc(measure = "OR",
-                                            ai = matching_type_disease,
-                                            bi = matching_type_carriage,
-                                            ci = non_matching_type_disease,
-                                            di = non_matching_type_carriage,
-                                            slab = study,
-                                            data = serotype_or_df)
-
-per_serotype_out <- dplyr::bind_rows(
-                    lapply(
-                      serotype_levels,
-                      per_serotype_estimate,
-                      serotype_effect_size_df
-                    ),
-                    lapply(
-                      serotype_levels,
-                      per_serotype_estimate,
-                      serotype_effect_size_df,
-                      method_type = "REML"
-                    )
-)
-
-sample_sizes <-
-  best_fitting_output %>%
-      dplyr::group_by(type) %>%
-      dplyr::mutate(num_samples = sum(carriage+disease)) %>%
-      dplyr::mutate(Sample_count = dplyr::case_when(
-                        num_samples < 11 ~ "0-10",
-                        num_samples < 51 ~ "11-50",
-                        num_samples < 101 ~ "51-100",
-                        TRUE ~ ">100"
-                      )
-                    ) %>%
-      dplyr::ungroup() %>%
-      dplyr::select(type, Sample_count) %>%
-      dplyr::distinct() %>%
-      dplyr::mutate(Sample_count = factor(Sample_count,
-                                          levels = c("0-10",
-                                                     "11-50",
-                                                     "51-100",
-                                                     ">100")))
-
-# Combine the invasiveness estimates
-combined_invasiveness_df <-
-  dplyr::bind_rows(
-    per_serotype_out %>%
-      dplyr::select(Analysis, Serotype, OR, OR_upper, OR_lower) %>%
-      dplyr::rename(Invasiveness = OR) %>%
-      dplyr::rename(Invasiveness_upper = OR_upper) %>%
-      dplyr::rename(Invasiveness_lower = OR_lower),
-    best_fitting_output %>%
-      dplyr::select(model_name, nu, nu_lower, nu_upper, type) %>%
-      dplyr::distinct() %>%
-      dplyr::rename(Analysis = model_name) %>%
-      dplyr::rename(Serotype = type) %>%
-      dplyr::rename(Invasiveness = nu) %>%
-      dplyr::rename(Invasiveness_upper = nu_upper) %>%
-      dplyr::rename(Invasiveness_lower = nu_lower)
-  ) %>%
-  tidyr::pivot_wider(id_cols = Serotype,
-                     names_from = Analysis,
-                     values_from = c(Invasiveness,Invasiveness_upper,Invasiveness_lower),
-                     names_sep = "_") %>%
-    dplyr::mutate("classification" = dplyr::case_when(
-        Serotype %in% vaccine_types[["PCV7"]] ~ "PCV7",
-        Serotype %in% vaccine_types[["PCV10"]] ~ "PCV10",
-        Serotype %in% vaccine_types[["PCV13"]] ~ "PCV13",
-        Serotype %in% vaccine_types[["PCV15"]] ~ "PCV15",
-        Serotype %in% vaccine_types[["PCV20"]] ~ "PCV20",
-        Serotype %in% vaccine_types[["PPV23"]] ~ "PPV23",
-        TRUE ~ "No PCV"
-      )
-    ) %>%
-  dplyr::left_join(sample_sizes, by = c("Serotype" = "type"))
-
-# Plot comparison of invasiveness estimates
-ggplot(combined_invasiveness_df,
-       aes(x = Invasiveness_adjusted_type_specific_poisson,
-           xmin = Invasiveness_lower_adjusted_type_specific_poisson,
-           xmax = Invasiveness_upper_adjusted_type_specific_poisson,
-           y = Invasiveness_FE,
-           ymin = Invasiveness_lower_FE,
-           ymax = Invasiveness_upper_FE,
-           colour = classification)) +
-  geom_errorbar(alpha = 0.25) +
-  geom_errorbarh(alpha = 0.25) +
-  geom_point() +
-  scale_x_continuous(trans = "log10") +
-  theme_bw() +
-  scale_color_manual(values = vaccine_colours) +
-  theme(legend.position = "bottom") +
-  ylab("Invasiveness estimated from log odds ratio") +
-  xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") +
-  facet_wrap(~Sample_count) +
-  stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson,
-               y = Invasiveness_FE),
-           inherit.aes = FALSE,
-           method = "kendall",
-           cor.coef.name = "tau") +
-  ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
-                                    dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
-                            aes(label = Serotype)
-                            )
-

-

-# Plot comparison of invasiveness estimates
-ggplot(combined_invasiveness_df,
-       aes(x = Invasiveness_adjusted_type_specific_poisson,
-           xmin = Invasiveness_lower_adjusted_type_specific_poisson,
-           xmax = Invasiveness_upper_adjusted_type_specific_poisson,
-           y = Invasiveness_REML,
-           ymin = Invasiveness_lower_REML,
-           ymax = Invasiveness_upper_REML,
-           colour = classification)) +
-  geom_errorbar(alpha = 0.25) +
-  geom_errorbarh(alpha = 0.25) +
-  geom_point() +
-  scale_x_continuous(trans = "log10") +
-  theme_bw() +
-  scale_color_manual(values = vaccine_colours) +
-  theme(legend.position = "bottom") +
-  ylab("Invasiveness estimated from log odds ratio") +
-  xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") +
-  facet_wrap(~Sample_count) +
-  stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson,
-               y = Invasiveness_REML),
-           inherit.aes = FALSE,
-           method = "kendall",
-           cor.coef.name = "tau") +
-  ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
-                                    dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
-                            aes(label = Serotype)
-                            )
-

+

+require(ggpubr)
+#> Loading required package: ggpubr
+#> 
+#> Attaching package: 'ggpubr'
+#> The following object is masked from 'package:cowplot':
+#> 
+#>     get_legend
+require(metafor)
+#> Loading required package: metafor
+#> Loading required package: Matrix
+#> 
+#> Attaching package: 'Matrix'
+#> The following objects are masked from 'package:tidyr':
+#> 
+#>     expand, pack, unpack
+#> 
+#> Loading the 'metafor' package (version 3.0-2). For an
+#> introduction to the package please type: help(metafor)
+
+get_serotype_stats <- function(serotype, df) {
+  sero_df <-
+    df %>%
+      tidyr::pivot_longer(c(carriage,disease),
+                          names_to = "clinical_manifestation",
+                          values_to = "observation") %>%
+      dplyr::group_by(study) %>%
+      dplyr::mutate(matching_type = dplyr::if_else(type == serotype,1,0)) %>%
+      dplyr::mutate(matching_type_disease =
+                      sum(observation[clinical_manifestation == "disease" & matching_type == 1])) %>%
+      dplyr::mutate(matching_type_carriage =
+                      sum(observation[clinical_manifestation == "carriage" & matching_type == 1])) %>%
+      dplyr::mutate(non_matching_type_disease =
+                      sum(observation[clinical_manifestation == "disease" & matching_type == 0])) %>%
+      dplyr::mutate(non_matching_type_carriage =
+                      sum(observation[clinical_manifestation == "carriage" & matching_type == 0])) %>%
+      dplyr::ungroup() %>%
+    dplyr::select(study,matching_type_disease,matching_type_carriage,non_matching_type_disease,non_matching_type_carriage) %>%
+    dplyr::distinct() %>%
+    dplyr::mutate(serotype = serotype) %>%
+    dplyr::filter(matching_type_carriage > 0 | matching_type_disease > 0)
+  return(sero_df)
+}
+
+per_serotype_estimate <- function(test_serotype, df, method_type = "FE") {
+  per_serotype_out <- metafor::rma(yi = yi,
+                                   vi = vi,
+                                   data = df,
+                                   slab = study,
+                                   subset = serotype == test_serotype,
+                                   method = method_type,
+                                   control=list(stepadj=0.5, maxiter=10000))
+  summary_df <-
+    data.frame(
+      "Analysis" = method_type,
+      "Serotype" = test_serotype,
+      "OR" = as.numeric(per_serotype_out$b),
+      "OR_upper" = per_serotype_out$ci.ub,
+      "OR_lower" = per_serotype_out$ci.lb,
+      "tau_squared" = per_serotype_out$tau2,
+      "i_squared" = per_serotype_out$I2,
+      "h_squared" = per_serotype_out$H2
+    )
+  return(summary_df)
+}
+
+serotype_or_df <- dplyr::bind_rows(lapply(
+                                   serotype_levels,
+                                   get_serotype_stats,
+                                   S_pneumoniae_adult_serotype)
+)
+
+serotype_effect_size_df <- metafor::escalc(measure = "OR",
+                                            ai = matching_type_disease,
+                                            bi = matching_type_carriage,
+                                            ci = non_matching_type_disease,
+                                            di = non_matching_type_carriage,
+                                            slab = study,
+                                            data = serotype_or_df)
+
+per_serotype_out <- dplyr::bind_rows(
+                    lapply(
+                      serotype_levels,
+                      per_serotype_estimate,
+                      serotype_effect_size_df
+                    ),
+                    lapply(
+                      serotype_levels,
+                      per_serotype_estimate,
+                      serotype_effect_size_df,
+                      method_type = "REML"
+                    )
+)
+
+sample_sizes <-
+  best_fitting_output %>%
+      dplyr::group_by(type) %>%
+      dplyr::mutate(num_samples = sum(carriage+disease)) %>%
+      dplyr::mutate(Sample_count = dplyr::case_when(
+                        num_samples < 11 ~ "0-10",
+                        num_samples < 51 ~ "11-50",
+                        num_samples < 101 ~ "51-100",
+                        TRUE ~ ">100"
+                      )
+                    ) %>%
+      dplyr::ungroup() %>%
+      dplyr::select(type, Sample_count) %>%
+      dplyr::distinct() %>%
+      dplyr::mutate(Sample_count = factor(Sample_count,
+                                          levels = c("0-10",
+                                                     "11-50",
+                                                     "51-100",
+                                                     ">100")))
+
+# Combine the invasiveness estimates
+combined_invasiveness_df <-
+  dplyr::bind_rows(
+    per_serotype_out %>%
+      dplyr::select(Analysis, Serotype, OR, OR_upper, OR_lower) %>%
+      dplyr::rename(Invasiveness = OR) %>%
+      dplyr::rename(Invasiveness_upper = OR_upper) %>%
+      dplyr::rename(Invasiveness_lower = OR_lower),
+    best_fitting_output %>%
+      dplyr::select(model_name, nu, nu_lower, nu_upper, type) %>%
+      dplyr::distinct() %>%
+      dplyr::rename(Analysis = model_name) %>%
+      dplyr::rename(Serotype = type) %>%
+      dplyr::rename(Invasiveness = nu) %>%
+      dplyr::rename(Invasiveness_upper = nu_upper) %>%
+      dplyr::rename(Invasiveness_lower = nu_lower)
+  ) %>%
+  tidyr::pivot_wider(id_cols = Serotype,
+                     names_from = Analysis,
+                     values_from = c(Invasiveness,Invasiveness_upper,Invasiveness_lower),
+                     names_sep = "_") %>%
+    dplyr::mutate("classification" = dplyr::case_when(
+        Serotype %in% vaccine_types[["PCV7"]] ~ "PCV7",
+        Serotype %in% vaccine_types[["PCV10"]] ~ "PCV10",
+        Serotype %in% vaccine_types[["PCV13"]] ~ "PCV13",
+        Serotype %in% vaccine_types[["PCV15"]] ~ "PCV15",
+        Serotype %in% vaccine_types[["PCV20"]] ~ "PCV20",
+        Serotype %in% vaccine_types[["PPV23"]] ~ "PPV23",
+        TRUE ~ "No PCV"
+      )
+    ) %>%
+  dplyr::left_join(sample_sizes, by = c("Serotype" = "type"))
+
+# Plot comparison of invasiveness estimates
+ggplot(combined_invasiveness_df,
+       aes(x = Invasiveness_adjusted_type_specific_negbin,
+           xmin = Invasiveness_lower_adjusted_type_specific_negbin,
+           xmax = Invasiveness_upper_adjusted_type_specific_negbin,
+           y = Invasiveness_FE,
+           ymin = Invasiveness_lower_FE,
+           ymax = Invasiveness_upper_FE,
+           colour = classification)) +
+  geom_errorbar(alpha = 0.25) +
+  geom_errorbarh(alpha = 0.25) +
+  geom_point() +
+  scale_x_continuous(trans = "log10") +
+  theme_bw() +
+  scale_color_manual(values = vaccine_colours) +
+  theme(legend.position = "bottom") +
+  ylab("Invasiveness estimated from log odds ratio") +
+  xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") +
+  facet_wrap(~Sample_count) +
+  stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin,
+               y = Invasiveness_FE),
+           inherit.aes = FALSE,
+           method = "kendall",
+           cor.coef.name = "tau") +
+  ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
+                                    dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
+                            aes(label = Serotype)
+                            )
+

+

+# Plot comparison of invasiveness estimates
+ggplot(combined_invasiveness_df,
+       aes(x = Invasiveness_adjusted_type_specific_negbin,
+           xmin = Invasiveness_lower_adjusted_type_specific_negbin,
+           xmax = Invasiveness_upper_adjusted_type_specific_negbin,
+           y = Invasiveness_REML,
+           ymin = Invasiveness_lower_REML,
+           ymax = Invasiveness_upper_REML,
+           colour = classification)) +
+  geom_errorbar(alpha = 0.25) +
+  geom_errorbarh(alpha = 0.25) +
+  geom_point() +
+  scale_x_continuous(trans = "log10") +
+  theme_bw() +
+  scale_color_manual(values = vaccine_colours) +
+  theme(legend.position = "bottom") +
+  ylab("Invasiveness estimated from log odds ratio") +
+  xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") +
+  facet_wrap(~Sample_count) +
+  stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin,
+               y = Invasiveness_REML),
+           inherit.aes = FALSE,
+           method = "kendall",
+           cor.coef.name = "tau") +
+  ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
+                                    dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
+                            aes(label = Serotype)
+                            )
+

Comparison with carriage duration

-

-carriage_duration.df <- data.frame(
-  "type" = c("19F","23F","6B","14","21","19B","18C","29","3","4","24F","NT","5","6A","6C"),
-  "carriage_duration" = c(46.9,21,16.2,7.2,1.6,-0.1,-1.9,-4.3,-4.5,-7.2,-8.5,-12.3,-18.6,0,0)
-)
-
-carriage_duration.df %<>%
-  dplyr::inner_join(pv_best_fitting_output,
-                    by = "type") %>%
-  dplyr::select(type,carriage_duration,classification,nu,nu_lower,nu_upper) %>%
-  dplyr::distinct()
-
-ggplot(carriage_duration.df,
-       aes(x = carriage_duration,
-           y = nu,
-           ymin = nu_lower,
-           ymax = nu_upper,
-           colour = classification)) +
-  geom_point() +
-  geom_errorbar() +
-  scale_colour_manual(values = vaccine_colours) +
-  ggrepel::geom_label_repel(aes(label = type)) +
-  scale_y_continuous(trans = "log10") +
-  theme_bw()
-

+

+carriage_duration.df <- data.frame(
+  "type" = c("19F","23F","6B","14","21","19B","18C","29","3","4","24F","NT","5","6A","6C"),
+  "carriage_duration" = c(46.9,21,16.2,7.2,1.6,-0.1,-1.9,-4.3,-4.5,-7.2,-8.5,-12.3,-18.6,0,0)
+)
+
+carriage_duration.df %<>%
+  dplyr::inner_join(pv_best_fitting_output,
+                    by = "type") %>%
+  dplyr::select(type,carriage_duration,classification,nu,nu_lower,nu_upper) %>%
+  dplyr::distinct()
+
+ggplot(carriage_duration.df,
+       aes(x = carriage_duration,
+           y = nu,
+           ymin = nu_lower,
+           ymax = nu_upper,
+           colour = classification)) +
+  geom_point() +
+  geom_errorbar() +
+  scale_colour_manual(values = vaccine_colours) +
+  ggrepel::geom_label_repel(aes(label = type)) +
+  scale_y_continuous(trans = "log10") +
+  theme_bw()
+

diff --git a/examples/s-pneumoniae-serotype-invasiveness.Rmd b/examples/s-pneumoniae-serotype-invasiveness.Rmd index 80a8fd4..abd2b66 100644 --- a/examples/s-pneumoniae-serotype-invasiveness.Rmd +++ b/examples/s-pneumoniae-serotype-invasiveness.Rmd @@ -29,8 +29,8 @@ require(xlsx) # Load stan package library(progressionEstimation) -pkgbuild::compile_dll() -roxygen2::roxygenize(package.dir = "..") +#pkgbuild::compile_dll() +#roxygen2::roxygenize(package.dir = "..") # Define serotype categories and palettes vaccine_types <- list( @@ -60,8 +60,8 @@ model_name_labels <- "null negative binomial", "type-specific Poisson", "type-specific negative binomial", - "study-adjusted null Poisson", - "study-adjusted null negative binomial", + "study-adjusted Poisson", + "study-adjusted negative binomial", "study-adjusted type-specific Poisson", "study-adjusted type-specific negative binomial" ) @@ -72,7 +72,7 @@ model_name_labels <- The dataset used in this analysis is contained in the `S_pneumoniae_infant_serotype` object, which includes data from `r S_pneumoniae_infant_serotype %>% dplyr::select(study) %>% dplyr::n_distinct()` studies on `r S_pneumoniae_infant_serotype %>% dplyr::select(type) %>% dplyr::n_distinct()` serotypes. The distribution of samples between each study can be plotted, if they are ranked by the mean number of carriage and disease isolates: -``` {r Plot distribution by study, include = FALSE} +``` {r Plot distribution by study} studies_by_size <- S_pneumoniae_infant_serotype %>% @@ -106,7 +106,7 @@ full_epi_data_plot <- The total number of observations for each serotype can be similarly plotted: -``` {r Plot distribution by serotype, include = FALSE} +``` {r Plot distribution by serotype} serotype_by_count <- S_pneumoniae_infant_serotype %>% @@ -145,7 +145,7 @@ serotype_frequency_plot <- ) ggsave(combined_full_epi_data_plot, - file = "full_epi_data_plot.png", + file = "full_epi_data_plot.pdf", height = 12, width = 8 ) @@ -154,7 +154,7 @@ ggsave(combined_full_epi_data_plot, As many of these serotypes are rare, to facilitate model fitting, we exclude any serotype for which the maximum number of observations is below five: -``` {r Plot distribution by serotype in filtered dataset, include = FALSE} +``` {r Plot distribution by serotype in filtered dataset} threshold_count <- 5 @@ -221,7 +221,7 @@ filtered_serotype_frequency_plot <- ) ggsave(combined_filtered_epi_data_plot, - file = "filtered_epi_data_plot.png", + file = "filtered_epi_data_plot.pdf", height = 12, width = 8 ) @@ -396,7 +396,7 @@ rhat_plots <- lapply(fit_list, plot_rhat) combined_rhat_plots <- cowplot::plot_grid(plotlist = rhat_plots, ncol = 4, nrow = 2, labels = "AUTO") ggsave(combined_rhat_plots, - file = "infant_combined_rhat_plots.png", + file = "infant_combined_rhat_plots.pdf", width = 8, height = 6) @@ -418,7 +418,7 @@ trace_plots <- lapply(fit_list, plot_lp) combined_trace_plots <- cowplot::plot_grid(plotlist = trace_plots, ncol = 4, nrow = 2, labels = "AUTO") ggsave(combined_trace_plots, - file = "infant_combined_trace_plots.png", + file = "infant_combined_trace_plots.pdf", width = 8, height = 6) @@ -455,7 +455,7 @@ pred_v_obs_plot <- rel_heights = c(1,0.1)) ggsave(pred_v_obs_plot, - file = "infant_serotypes_pred_v_obs_plot.png", + file = "infant_serotypes_pred_v_obs_plot.pdf", height = 20, width = 10) @@ -506,7 +506,7 @@ obs_pred_df <- ) ggsave(serotype_rmse_plot, - file = "serotype_rmse_plot.png", + file = "serotype_rmse_plot.pdf", width = 7, height = 7 ) @@ -537,7 +537,7 @@ The fits of the negative binomial can be evaluated through plotting the estimate ) ggsave(phi_plot, - file="serotype_phi_plot.png", + file="serotype_phi_plot.pdf", height = 6, width = 6) @@ -547,7 +547,7 @@ ggsave(phi_plot, The model likelihoods can be compared using leave-one-out cross-validation: -``` {r Comparison with LOO-CV using full log likelihood, include = FALSE} +``` {r Comparison with LOO-CV using full log likelihood} loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list, use_moments = FALSE, @@ -557,11 +557,16 @@ loo_comparison %>% kableExtra::kable() %>% kableExtra::kable_styling(latex_options = "scale_down") +write.csv(loo_comparison, + file = "child_serotype_loo_comparison.csv", + quote = FALSE, + row.names = FALSE) + ``` The Pareto distribution k values are too high for robust estimates of the ELPD. This reflects many of the points being -``` {r Comparison with LOO-CV using disease distribution log likelihood, include = FALSE} +``` {r Comparison with LOO-CV using disease distribution log likelihood} disease_loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list, log_lik_param = "disease_log_lik", @@ -572,21 +577,33 @@ disease_loo_comparison %>% kableExtra::kable() %>% kableExtra::kable_styling(latex_options = "scale_down") +write.csv(disease_loo_comparison, + file = "child_disease_serotype_loo_comparison.csv", + quote = FALSE, + row.names = FALSE) + ``` ## Run model comparison with Bayes factors As the models can instead be compared with Bayes factors: -``` {r Comparison with BF, include = FALSE} +``` {r Comparison with BF} + +bf_comparison <- + progressionEstimation::compare_model_fits_with_bf(fit_list, + num_iter = n_iter, + num_threads = n_core) -bf_comparison <- progressionEstimation::compare_model_fits_with_bf(fit_list, - num_iter = n_iter, - num_threads = n_core) bf_comparison %>% kableExtra::kable() %>% kableExtra::kable_styling(latex_options = "scale_down") +write.csv(bf_comparison, + file = "child_disease_serotype_bf_comparison.csv", + quote = FALSE, + row.names = FALSE) + ``` ## Plot serotype invasiveness @@ -602,18 +619,18 @@ full_infant_serotype_invasiveness <- ) ) -full_adjusted_type_specific_poisson_fit <- +full_adjusted_type_specific_negbin_fit <- progressionEstimation::fit_progression_rate_model(full_infant_serotype_invasiveness, type_specific = TRUE, location_adjustment = TRUE, - stat_model = "poisson", + stat_model = "negbin", num_chains = n_chains, num_iter = n_iter, num_cores = n_core) -rhat_plot <- plot(full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005) +rhat_plot <- plot(full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005) -trace_plot <- rstan::traceplot(full_adjusted_type_specific_poisson_fit, pars = "lp__") + +trace_plot <- rstan::traceplot(full_adjusted_type_specific_negbin_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90)) best_fitting_model_validation_plot <- cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot), @@ -622,7 +639,7 @@ best_fitting_model_validation_plot <- cowplot::plot_grid(plotlist = list(rhat_pl labels = "AUTO") ggsave(best_fitting_model_validation_plot, - file = "best_fitting_infant_model_validation_plot.png", + file = "best_fitting_infant_model_validation_plot.pdf", width = 8, height = 6) @@ -634,7 +651,7 @@ mixedrank = function(x) order(gtools::mixedorder(as.character(x))) # Annotate serotypes by status best_fitting_output <- - progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_poisson_fit, + progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_negbin_fit, S_pneumoniae_infant_serotype) %>% dplyr::mutate("classification" = dplyr::case_when( type %in% vaccine_types[["PCV7"]] ~ "PCV7", @@ -679,12 +696,12 @@ best_fitting_output %<>% use_sample_size = TRUE)) ggsave(invasiveness_plot, - file = "full_serotype_invasiveness_plot.png", + file = "full_serotype_invasiveness_plot.pdf", height = 8, width = 8) write.csv(best_fitting_output, - file = "study_adjusted_type_specific_poisson_serotype_fit.csv", + file = "study_adjusted_type_specific_negbin_serotype_fit.csv", quote = F, row.names = F) @@ -707,6 +724,11 @@ write.csv(best_fitting_output %>% (scale_factor_plot <- progressionEstimation::plot_study_scale_factors(best_fitting_output)) +ggsave(scale_factor_plot, + file = "serotype_scale_factor_plot.png", + width = 8, + height = 6) + ``` ## Compare a model fit that account for PCVs protecting against disease @@ -736,18 +758,18 @@ pv_S_pneumoniae_infant_serotype %<>% pv_full_infant_serotype_invasiveness <- progressionEstimation::process_input_data(pv_S_pneumoniae_infant_serotype) -pv_full_adjusted_type_specific_poisson_fit <- +pv_full_adjusted_type_specific_negbin_fit <- progressionEstimation::fit_progression_rate_model(pv_full_infant_serotype_invasiveness, type_specific = TRUE, location_adjustment = TRUE, - stat_model = "poisson", + stat_model = "negbin", num_chains = n_chains, num_iter = n_iter, num_cores = n_core) -rhat_plot <- plot(pv_full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005) +rhat_plot <- plot(pv_full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005) -trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_poisson_fit, pars = "lp__") + +trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_negbin_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90, size = 8)) best_fitting_pv_model_validation_plot <- @@ -757,7 +779,7 @@ best_fitting_pv_model_validation_plot <- labels = "AUTO") ggsave(best_fitting_pv_model_validation_plot, - file = "best_fitting_pv_infant_model_validation_plot.png", + file = "best_fitting_pv_infant_model_validation_plot.pdf", width = 8, height = 6) @@ -767,7 +789,7 @@ ggsave(best_fitting_pv_model_validation_plot, pv_best_fitting_output <- progressionEstimation::process_progression_rate_model_output( - pv_full_adjusted_type_specific_poisson_fit, pv_S_pneumoniae_infant_serotype) %>% + pv_full_adjusted_type_specific_negbin_fit, pv_S_pneumoniae_infant_serotype) %>% dplyr::mutate("classification" = dplyr::case_when( gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7", gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10", @@ -820,7 +842,7 @@ pv_best_fitting_output %<>% ) ggsave(joint_invasiveness_plot, - file = "joint_infant_serotype_plot.png", + file = "joint_infant_serotype_plot.pdf", height = 10, width = 9) @@ -970,9 +992,9 @@ combined_invasiveness_df <- # Plot comparison of invasiveness estimates (fixed_effects_comparison <- ggplot(combined_invasiveness_df, - aes(x = Invasiveness_adjusted_type_specific_poisson, - xmin = Invasiveness_lower_adjusted_type_specific_poisson, - xmax = Invasiveness_upper_adjusted_type_specific_poisson, + aes(x = Invasiveness_adjusted_type_specific_negbin, + xmin = Invasiveness_lower_adjusted_type_specific_negbin, + xmax = Invasiveness_upper_adjusted_type_specific_negbin, y = Invasiveness_FE, ymin = Invasiveness_lower_FE, ymax = Invasiveness_upper_FE, @@ -985,15 +1007,15 @@ combined_invasiveness_df <- scale_color_manual(values = vaccine_colours) + theme(legend.position = "bottom") + ylab("Invasiveness estimated from log odds ratio") + - xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") + + xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") + facet_wrap(~Sample_count) + - stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson, + stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin, y = Invasiveness_FE), inherit.aes = FALSE, method = "kendall", cor.coef.name = "tau") + ggrepel::geom_label_repel(data = combined_invasiveness_df %>% - dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), + dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), aes(label = Serotype) ) ) @@ -1005,9 +1027,9 @@ combined_invasiveness_df <- # Plot comparison of invasiveness estimates (random_effects_comparison <- ggplot(combined_invasiveness_df, - aes(x = Invasiveness_adjusted_type_specific_poisson, - xmin = Invasiveness_lower_adjusted_type_specific_poisson, - xmax = Invasiveness_upper_adjusted_type_specific_poisson, + aes(x = Invasiveness_adjusted_type_specific_negbin, + xmin = Invasiveness_lower_adjusted_type_specific_negbin, + xmax = Invasiveness_upper_adjusted_type_specific_negbin, y = Invasiveness_REML, ymin = Invasiveness_lower_REML, ymax = Invasiveness_upper_REML, @@ -1020,15 +1042,15 @@ combined_invasiveness_df <- scale_color_manual(values = vaccine_colours) + theme(legend.position = "bottom") + ylab("Invasiveness estimated from log odds ratio") + - xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") + + xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") + facet_wrap(~Sample_count) + - stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson, + stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin, y = Invasiveness_REML), inherit.aes = FALSE, method = "kendall", cor.coef.name = "tau") + ggrepel::geom_label_repel(data = combined_invasiveness_df %>% - dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), + dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"), aes(label = Serotype) ) ) @@ -1044,7 +1066,7 @@ combined_odds_ratio_plot <- ) ggsave(combined_odds_ratio_plot, - file = "combined_odds_ratio_plot.png", + file = "combined_odds_ratio_plot.pdf", width = 8, height = 12) @@ -1056,7 +1078,7 @@ This comparison can be extended to location-specific invasiveness factors, which netherland_pre_pcv_invasiveness_df <- progressionEstimation::get_type_invasiveness_for_study(S_pneumoniae_infant_serotype, - full_adjusted_type_specific_poisson_fit, + full_adjusted_type_specific_negbin_fit, study = "Netherlands.post.PCV10") netherland_pre_pcv_invasiveness_df %<>% @@ -1135,9 +1157,9 @@ netherlands_or_comparison_df <- scale_color_manual(values = vaccine_colours) + theme(legend.position = "bottom") + ylab("Invasiveness estimated from log odds ratio") + - xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") + + xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") + facet_wrap(~Sample_count) + - stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson, + stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin, y = Invasiveness_FE), inherit.aes = FALSE, method = "kendall", @@ -1168,9 +1190,9 @@ The same comparison can be undertaken against odds ratios calculated with random scale_color_manual(values = vaccine_colours) + theme(legend.position = "bottom") + ylab("Invasiveness estimated from log odds ratio") + - xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") + + xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") + facet_wrap(~Sample_count) + - stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson, + stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin, y = Invasiveness_REML), inherit.aes = FALSE, method = "kendall", @@ -1185,7 +1207,7 @@ combined_netherlands_or_comparison_plot <- labels = "AUTO") ggsave(combined_netherlands_or_comparison_plot, - file = "netherlands_or_comparison.png", + file = "netherlands_or_comparison.pdf", height = 8, width = 14) @@ -1224,7 +1246,7 @@ carriage_duration.df %<>% ) ggsave(invasiveness_v_duration_plot, - file = "invasiveness_v_duration.png", + file = "invasiveness_v_duration.pdf", height = 8, width = 8) diff --git a/examples/s-pneumoniae-serotype-invasiveness.html b/examples/s-pneumoniae-serotype-invasiveness.html index 2cb1ea9..2f92ed4 100644 --- a/examples/s-pneumoniae-serotype-invasiveness.html +++ b/examples/s-pneumoniae-serotype-invasiveness.html @@ -14,230 +14,9 @@ s-pneumoniae-serotype-invasiveness - - + + + + @@ -542,119 +143,252 @@

s-pneumoniae-serotype-invasiveness

-
# Load dependencies
-require(tidyverse)
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-#> options(mc.cores = parallel::detectCores()).
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-#> rstan_options(auto_write = TRUE)
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-require(loo)
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-#> This is loo version 2.4.1
-#> - Online documentation and vignettes at mc-stan.org/loo
-#> - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
-#> 
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-require(ggrepel)
-#> Loading required package: ggrepel
-require(xlsx)
-#> Loading required package: xlsx
-
-# Load stan package
-library(progressionEstimation)
-pkgbuild::compile_dll()
-roxygen2::roxygenize(package.dir = "..")
-#> ℹ Loading progressionEstimation
-#> Loading required package: kableExtra
-#> 
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-#> Writing NAMESPACE
-#> Writing NAMESPACE
-
-# Define serotype categories and palettes
-vaccine_types <- list(
-  "PCV7" = c("4","6B","9V","14","18C","19F","23F"),
-  "PCV10" = c("1","5","7F"),
-  "PCV13" = c("6A","3","19A"),
-  "PCV15" = c("22F","33F"),
-  "PCV20" = c("8","10A","11A","12F","15B/C"),
-  "PPV23" = c("2","9N","17F","20")
-)
-
-vaccine_colours <- c("No PCV" = "blue",
-                     "PCV7" = "red",
-                     "PCV10" = "orange",
-                     "PCV13" = "coral2",
-                     "PCV15" = "pink",
-                     "PCV20" = "purple",
-                     "PPV23" = "black")
-
-epi_colors <- c(
-  "carriage" = "skyblue",
-  "disease" = "cornflowerblue"
-)
-
-model_name_labels <-
-  c("null Poisson",
-    "null negative binomial",
-    "type-specific Poisson",
-    "type-specific negative binomial",
-    "study-adjusted null Poisson",
-    "study-adjusted null negative binomial",
-    "study-adjusted type-specific Poisson",
-    "study-adjusted type-specific negative binomial"
-  )
+
# Load dependencies
+require(tidyverse)
+#> Loading required package: tidyverse
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+#> For execution on a local, multicore CPU with excess RAM we recommend calling
+#> options(mc.cores = parallel::detectCores()).
+#> To avoid recompilation of unchanged Stan programs, we recommend calling
+#> rstan_options(auto_write = TRUE)
+#> 
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+#> Loading required package: bridgesampling
+require(loo)
+#> Loading required package: loo
+#> This is loo version 2.4.1
+#> - Online documentation and vignettes at mc-stan.org/loo
+#> - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
+#> 
+#> Attaching package: 'loo'
+#> The following object is masked from 'package:rstan':
+#> 
+#>     loo
+require(cowplot)
+#> Loading required package: cowplot
+require(ggrepel)
+#> Loading required package: ggrepel
+require(xlsx)
+#> Loading required package: xlsx
+
+# Load stan package
+library(progressionEstimation)
+#pkgbuild::compile_dll()
+#roxygen2::roxygenize(package.dir = "..")
+
+# Define serotype categories and palettes
+vaccine_types <- list(
+  "PCV7" = c("4","6B","9V","14","18C","19F","23F"),
+  "PCV10" = c("1","5","7F"),
+  "PCV13" = c("6A","3","19A"),
+  "PCV15" = c("22F","33F"),
+  "PCV20" = c("8","10A","11A","12F","15B/C"),
+  "PPV23" = c("2","9N","17F","20")
+)
+
+vaccine_colours <- c("No PCV" = "blue",
+                     "PCV7" = "red",
+                     "PCV10" = "orange",
+                     "PCV13" = "coral2",
+                     "PCV15" = "pink",
+                     "PCV20" = "purple",
+                     "PPV23" = "black")
+
+epi_colors <- c(
+  "carriage" = "skyblue",
+  "disease" = "cornflowerblue"
+)
+
+model_name_labels <-
+  c("null Poisson",
+    "null negative binomial",
+    "type-specific Poisson",
+    "type-specific negative binomial",
+    "study-adjusted null Poisson",
+    "study-adjusted null negative binomial",
+    "study-adjusted type-specific Poisson",
+    "study-adjusted type-specific negative binomial"
+  )

Description and filtering of the dataset

The dataset used in this analysis is contained in the S_pneumoniae_infant_serotype object, which includes data from 20 studies on 72 serotypes. The distribution of samples between each study can be plotted, if they are ranked by the mean number of carriage and disease isolates:

+

+studies_by_size <-
+  S_pneumoniae_infant_serotype %>%
+    group_by(study) %>%
+    dplyr::mutate(total_count = sum(carriage)+sum(disease)) %>%
+    dplyr::select(study,total_count) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(total_count)) %>%
+    dplyr::select(study) %>%
+    dplyr::pull()
+
+S_pneumoniae_infant_serotype %<>%
+  dplyr::mutate(study = factor(study, levels = studies_by_size))
+
+full_epi_data_plot <-
+  ggplot(S_pneumoniae_infant_serotype %>%
+           tidyr::pivot_longer(c(carriage,disease),
+                               names_to = "Sample type",
+                               values_to = "count"),
+         aes(x = study,
+             y = count,
+             colour = `Sample type`,
+             fill = `Sample type`)) +
+    geom_col() +
+    theme_bw() + 
+    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
+    scale_fill_manual(values = epi_colors) +
+    scale_colour_manual(values = epi_colors)

The total number of observations for each serotype can be similarly plotted:

+

+serotype_by_count <-
+  S_pneumoniae_infant_serotype %>%
+    group_by(type) %>%
+    dplyr::mutate(total_count = sum(carriage)+sum(disease)) %>%
+    dplyr::select(type,total_count) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(total_count)) %>%
+    dplyr::select(type) %>%
+    dplyr::pull()
+
+S_pneumoniae_infant_serotype %<>%
+  dplyr::mutate(type = factor(type, levels = serotype_by_count))
+
+serotype_frequency_plot <-
+  ggplot(S_pneumoniae_infant_serotype %>%
+           tidyr::pivot_longer(c(carriage,disease),
+                               names_to = "Sample type",
+                               values_to = "count"),
+         aes(x = type,
+             y = count,
+             colour = `Sample type`,
+             fill = `Sample type`)) +
+    geom_col() +
+    xlab("Serotype") +
+    theme_bw() + 
+    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
+    scale_fill_manual(values = epi_colors) +
+    scale_colour_manual(values = epi_colors)
+
+(combined_full_epi_data_plot <-
+  cowplot::plot_grid(plotlist = list(full_epi_data_plot, serotype_frequency_plot),
+                     nrow = 2,
+                     ncol = 1,
+                     labels = "AUTO")
+)
+

+

+ggsave(combined_full_epi_data_plot,
+       file = "full_epi_data_plot.pdf",
+       height = 12,
+       width = 8
+)

As many of these serotypes are rare, to facilitate model fitting, we exclude any serotype for which the maximum number of observations is below five:

+

+threshold_count <- 5
+
+filtered_S_pneumoniae_infant_serotype <-
+  S_pneumoniae_infant_serotype %>%
+    dplyr::filter(carriage >= threshold_count | disease >= threshold_count)
+# %>%
+#     dplyr::group_by(type)%>%
+#     dplyr::mutate(study_count = n()) %>%
+#     dplyr::ungroup() %>%
+#     dplyr::filter(study_count > threshold_count) %>%
+#     dplyr::group_by(study) %>%
+#     dplyr::mutate(serotype_count = n()) %>%
+#     dplyr::ungroup() %>%
+#     dplyr::filter(serotype_count > threshold_count) %>%
+#     dplyr::mutate(type = factor(type))
+
+filtered_S_pneumoniae_infant_serotype %<>%
+    dplyr::mutate(study = factor(study, levels = studies_by_size[studies_by_size %in% unique(filtered_S_pneumoniae_infant_serotype$study)]))
+
+filtered_S_pneumoniae_infant_serotype %<>%
+    dplyr::mutate(type = factor(type,
+                                          levels = serotype_by_count[serotype_by_count %in% unique(filtered_S_pneumoniae_infant_serotype$type)]))
+
+infant_serotype_invasiveness <- 
+  progressionEstimation::process_input_data(filtered_S_pneumoniae_infant_serotype)
+
+filtered_epi_data_plot <-
+    ggplot(filtered_S_pneumoniae_infant_serotype %>%
+           tidyr::pivot_longer(c(carriage,disease),
+                               names_to = "Sample type",
+                               values_to = "count"),
+         aes(x = study,
+             y = count,
+             colour = `Sample type`,
+             fill = `Sample type`)) +
+    geom_col() +
+    theme_bw() + 
+    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
+    scale_fill_manual(values = epi_colors) +
+    scale_colour_manual(values = epi_colors)
+
+filtered_serotype_frequency_plot <-
+  ggplot(filtered_S_pneumoniae_infant_serotype %>%
+           tidyr::pivot_longer(c(carriage,disease),
+                               names_to = "Sample type",
+                               values_to = "count"),
+         aes(x = type,
+             y = count,
+             colour = `Sample type`,
+             fill = `Sample type`)) +
+    geom_col() +
+    xlab("Serotype") +
+    theme_bw() + 
+    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
+    scale_fill_manual(values = epi_colors) +
+    scale_colour_manual(values = epi_colors)
+
+(combined_filtered_epi_data_plot <-
+  cowplot::plot_grid(plotlist = list(filtered_epi_data_plot, filtered_serotype_frequency_plot),
+                     nrow = 2,
+                     ncol = 1,
+                     labels = "AUTO")
+)
+

+

+ggsave(combined_filtered_epi_data_plot,
+       file = "filtered_epi_data_plot.pdf",
+       height = 12,
+       width = 8
+)

This filtered dataset comprises 72 serotypes.

Fitting the statistical models

-

The null model, in which each serotyoe \(j\) causes invasive disease at the same rate in each location \(i\), can be fitted using a Poisson distribution of disease isolates (null Poisson model):

+

The null model, in which each serotype \(j\) causes invasive disease at the same rate in each location \(i\), can be fitted using a Poisson distribution of disease isolates (null Poisson model):

\[d_{i,j} \sim Pois(\nu\rho_{i,j}N_{i}t_{i})\]

The null model can be fitted using a negative binomial distribution of disease isolates (null negative binomial model):

\[d_{i,j} \sim NegBin(\nu\rho_{i,j}N_{i}t_{i},\phi)\]

@@ -671,791 +405,1480 @@

Fitting the statistical models

This can also be used with the negative binomial model (adjusted type-specific negative binomial model):

\[d_{i,j} \sim NegBin(\delta_{i}\nu_{j}\rho_{i,j}N_{i}t_{i},\phi)\]

To check the models have fitted correctly, we can plot the \(\hat{R}\) values across MCMCs:

-

-fit_list <- list(null_poisson_fit,
-                 null_negbin_fit,
-                 type_specific_poisson_fit,
-                 type_specific_negbin_fit,
-                 adjusted_poisson_fit,
-                 adjusted_negbin_fit,
-                 adjusted_type_specific_poisson_fit,
-                 adjusted_type_specific_negbin_fit)
-
-plot_rhat <- function(fit) {
-  rhat_plot <- plot(fit, plotfun = "rhat", binwidth = 0.00005) +
-                theme(axis.text.x = element_text(angle = 90))
-  return(rhat_plot)
-}
-
-rhat_plots <- lapply(fit_list, plot_rhat)
-
-combined_rhat_plots <- cowplot::plot_grid(plotlist = rhat_plots, ncol = 4, nrow = 2, labels = "AUTO")
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-ggsave(combined_rhat_plots,
-       file = "infant_combined_rhat_plots.png",
-       width = 8,
-       height = 6)
+

+fit_list <- list(null_poisson_fit,
+                 null_negbin_fit,
+                 type_specific_poisson_fit,
+                 type_specific_negbin_fit,
+                 adjusted_poisson_fit,
+                 adjusted_negbin_fit,
+                 adjusted_type_specific_poisson_fit,
+                 adjusted_type_specific_negbin_fit)
+
+plot_rhat <- function(fit) {
+  rhat_plot <- plot(fit, plotfun = "rhat", binwidth = 0.00005) +
+                theme(axis.text.x = element_text(angle = 90))
+  return(rhat_plot)
+}
+
+rhat_plots <- lapply(fit_list, plot_rhat)
+
+combined_rhat_plots <- cowplot::plot_grid(plotlist = rhat_plots, ncol = 4, nrow = 2, labels = "AUTO")
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+ggsave(combined_rhat_plots,
+       file = "infant_combined_rhat_plots.pdf",
+       width = 8,
+       height = 6)

Convergence can also be checked using trace plots of the log likelihood values:

-

-plot_lp <- function(fit) {
-  pl <- rstan::traceplot(fit, pars = "lp__")
-  no_leg_pl <- pl + theme(legend.position = "none",
-                          axis.text.x = element_text(angle = 90))
-  return(no_leg_pl)
-}
-
-trace_plots <- lapply(fit_list, plot_lp)
-
-combined_trace_plots <- cowplot::plot_grid(plotlist = trace_plots, ncol = 4, nrow = 2, labels = "AUTO")
-
-ggsave(combined_trace_plots,
-       file = "infant_combined_trace_plots.png",
-       width = 8,
-       height = 6)
+

+plot_lp <- function(fit) {
+  pl <- rstan::traceplot(fit, pars = "lp__")
+  no_leg_pl <- pl + theme(legend.position = "none",
+                          axis.text.x = element_text(angle = 90))
+  return(no_leg_pl)
+}
+
+trace_plots <- lapply(fit_list, plot_lp)
+
+combined_trace_plots <- cowplot::plot_grid(plotlist = trace_plots, ncol = 4, nrow = 2, labels = "AUTO")
+
+ggsave(combined_trace_plots,
+       file = "infant_combined_trace_plots.pdf",
+       width = 8,
+       height = 6)

Compare model observations and predictions

For each model, the output can be processed, and the observations plotted against each model’s predictions.

-

-model_outputs <- lapply(fit_list,
-                        progressionEstimation::process_progression_rate_model_output,
-                        filtered_S_pneumoniae_infant_serotype)
-
-prediction_plots <- lapply(model_outputs,
-                           progressionEstimation::plot_case_carrier_predictions,
-                           legend = FALSE,
-                           n_label = 0)
-
-no_leg_plot <- cowplot::plot_grid(plotlist = prediction_plots,
-                                  ncol = 1,
-                                  nrow = 8,
-                                  labels = "AUTO",
-                                  vjust = -0.01) +
-      theme(plot.margin = unit(c(0.5,0,0,0), "cm"))
-
-prediction_plot_legend <- progressionEstimation::plot_case_carrier_predictions(model_outputs[[1]], just_legend = TRUE) 
-
-pred_v_obs_plot <- 
-  cowplot::plot_grid(no_leg_plot,
-                     prediction_plot_legend,
-                     ncol = 1,
-                     rel_heights = c(1,0.1))
-
-ggsave(pred_v_obs_plot,
-       file = "infant_serotypes_pred_v_obs_plot.png",
-       height = 20,
-       width = 10)
+

+model_outputs <- lapply(fit_list,
+                        progressionEstimation::process_progression_rate_model_output,
+                        filtered_S_pneumoniae_infant_serotype)
+
+prediction_plots <- lapply(model_outputs,
+                           progressionEstimation::plot_case_carrier_predictions,
+                           legend = FALSE,
+                           n_label = 0)
+
+no_leg_plot <- cowplot::plot_grid(plotlist = prediction_plots,
+                                  ncol = 1,
+                                  nrow = 8,
+                                  labels = "AUTO",
+                                  vjust = -0.01) +
+      theme(plot.margin = unit(c(0.5,0,0,0), "cm"))
+
+prediction_plot_legend <- progressionEstimation::plot_case_carrier_predictions(model_outputs[[1]], just_legend = TRUE) 
+
+pred_v_obs_plot <- 
+  cowplot::plot_grid(no_leg_plot,
+                     prediction_plot_legend,
+                     ncol = 1,
+                     rel_heights = c(1,0.1))
+
+ggsave(pred_v_obs_plot,
+       file = "infant_serotypes_pred_v_obs_plot.pdf",
+       height = 20,
+       width = 10)

The deviation of the predicted and observed values can be simply evaluated using the root mean square error:

-

-obs_pred_df <-
-  dplyr::bind_rows(model_outputs) %>%
-  dplyr::select(model_name,carriage_rmse,disease_rmse,phi,phi_lower,phi_upper) %>%
-  tidyr::pivot_longer(c(carriage_rmse,disease_rmse), names_to = "Observation", values_to = "RMSE") %>%
-  dplyr::mutate(model_name = factor(model_name,
-                                    levels = c(
-                                      "null_poisson",
-                                      "null_negbin",
-                                      "type_specific_poisson",
-                                      "type_specific_negbin",
-                                      "adjusted_null_poisson",
-                                      "adjusted_null_negbin",
-                                      "adjusted_type_specific_poisson",
-                                      "adjusted_type_specific_negbin"
-                                      )
-                                    )
-                ) %>%
-  dplyr::mutate(Observation = dplyr::case_when(
-                    Observation == "carriage_rmse" ~ "Carriage",
-                    Observation == "disease_rmse" ~ "Disease"
-                  )
-                )
-
-(serotype_rmse_plot <-
-  ggplot(obs_pred_df, aes(x = model_name, y = RMSE)) +
-    #geom_boxplot(outlier.shape = NA) +
-    geom_point(position = position_jitter(width = 0.25),
-               alpha = 0.25,
-               cex = 0.75,
-               colour = "blue",
-               pch = 4) +
-    geom_violin(fill = NA) +
-    scale_y_continuous(trans="log10") +
-    theme_bw() +
-    facet_grid(Observation ~ .) +
-    scale_x_discrete(labels = model_name_labels) +
-    xlab("Model name") +
-    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
-)
-

-

-ggsave(serotype_rmse_plot,
-       file = "serotype_rmse_plot.png",
-       width = 7,
-       height = 7
-)
+

+obs_pred_df <-
+  dplyr::bind_rows(model_outputs) %>%
+  dplyr::select(model_name,carriage_rmse,disease_rmse,phi,phi_lower,phi_upper) %>%
+  tidyr::pivot_longer(c(carriage_rmse,disease_rmse), names_to = "Observation", values_to = "RMSE") %>%
+  dplyr::mutate(model_name = factor(model_name,
+                                    levels = c(
+                                      "null_poisson",
+                                      "null_negbin",
+                                      "type_specific_poisson",
+                                      "type_specific_negbin",
+                                      "adjusted_null_poisson",
+                                      "adjusted_null_negbin",
+                                      "adjusted_type_specific_poisson",
+                                      "adjusted_type_specific_negbin"
+                                      )
+                                    )
+                ) %>%
+  dplyr::mutate(Observation = dplyr::case_when(
+                    Observation == "carriage_rmse" ~ "Carriage",
+                    Observation == "disease_rmse" ~ "Disease"
+                  )
+                )
+
+(serotype_rmse_plot <-
+  ggplot(obs_pred_df, aes(x = model_name, y = RMSE)) +
+    #geom_boxplot(outlier.shape = NA) +
+    geom_point(position = position_jitter(width = 0.25),
+               alpha = 0.25,
+               cex = 0.75,
+               colour = "blue",
+               pch = 4) +
+    geom_violin(fill = NA) +
+    scale_y_continuous(trans="log10") +
+    theme_bw() +
+    facet_grid(Observation ~ .) +
+    scale_x_discrete(labels = model_name_labels) +
+    xlab("Model name") +
+    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+)
+

+

+ggsave(serotype_rmse_plot,
+       file = "serotype_rmse_plot.pdf",
+       width = 7,
+       height = 7
+)

The fits of the negative binomial can be evaluated through plotting the estimates of the precision parameter, \(\phi\). As \(\phi\) increases, the variance of the negative binomial distribution decreases, and the negative binomal model becomes more similar to the Poisson model.

-
(phi_plot <-
-  ggplot(obs_pred_df %>%
-          dplyr::filter(!is.na(phi)) %>%
-          dplyr::group_by(model_name) %>%
-          dplyr::slice(1) %>%
-          dplyr::ungroup(),
-        aes(x = model_name,
-            y = phi,
-            ymin = phi_lower,
-            ymax = phi_upper)) +
-    geom_point() +
-    geom_errorbar(width = 0.25) +
-    theme_bw() +
-    scale_y_continuous(trans="log10") +
-    ylab(expression(phi)) +
-    xlab("Model name") +
-    scale_x_discrete(labels = model_name_labels[c(2,4,6,8)]) +
-    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
-)
-

-

-ggsave(phi_plot,
-       file="serotype_phi_plot.png",
-       height = 6,
-       width = 6)
+
(phi_plot <-
+  ggplot(obs_pred_df %>%
+          dplyr::filter(!is.na(phi)) %>%
+          dplyr::group_by(model_name) %>%
+          dplyr::slice(1) %>%
+          dplyr::ungroup(),
+        aes(x = model_name,
+            y = phi,
+            ymin = phi_lower,
+            ymax = phi_upper)) +
+    geom_point() +
+    geom_errorbar(width = 0.25) +
+    theme_bw() +
+    scale_y_continuous(trans="log10") +
+    ylab(expression(phi)) +
+    xlab("Model name") +
+    scale_x_discrete(labels = model_name_labels[c(2,4,6,8)]) +
+    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+)
+

+

+ggsave(phi_plot,
+       file="serotype_phi_plot.pdf",
+       height = 6,
+       width = 6)

Run model comparison with leave-one-out cross-validation

The model likelihoods can be compared using leave-one-out cross-validation:

+

+loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list,
+                                                                     use_moments = FALSE,
+                                                                     num_threads = n_core)
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+loo_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +elpd_diff + +se_diff + +elpd_loo + +se_elpd_loo + +p_loo + +se_p_loo + +looic + +se_looic +
+adjusted_type_specific_poisson + +0.0000 + +0.00000 + +-1780.689 + +33.23288 + +387.4526 + +11.031127 + +3561.378 + +66.46575 +
+adjusted_type_specific_negbin + +-13.5003 + +14.55242 + +-1794.189 + +25.17121 + +357.1155 + +5.459380 + +3588.379 + +50.34242 +
+type_specific_negbin + +-190.5071 + +23.01549 + +-1971.196 + +27.92854 + +343.1917 + +5.737811 + +3942.392 + +55.85708 +
+adjusted_null_negbin + +-239.4094 + +25.27035 + +-2020.098 + +30.52012 + +324.3351 + +5.736621 + +4040.197 + +61.04023 +
+null_negbin + +-288.2935 + +24.83839 + +-2068.983 + +30.23868 + +299.4660 + +3.162663 + +4137.965 + +60.47737 +
+adjusted_null_poisson + +-917.0691 + +111.26184 + +-2697.758 + +125.59723 + +457.3265 + +29.991526 + +5395.516 + +251.19446 +
+type_specific_poisson + +-950.4216 + +144.79549 + +-2731.111 + +158.51865 + +564.7518 + +36.669220 + +5462.221 + +317.03729 +
+null_poisson + +-1931.6442 + +223.90635 + +-3712.333 + +236.83557 + +311.9120 + +6.839573 + +7424.666 + +473.67113 +
+

+write.csv(loo_comparison,
+          file = "child_serotype_loo_comparison.csv",
+          quote = FALSE,
+          row.names = FALSE)

The Pareto distribution k values are too high for robust estimates of the ELPD. This reflects many of the points being

+

+disease_loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list,
+                                                                     log_lik_param = "disease_log_lik",
+                                                                     use_moments = FALSE,
+                                                                     num_threads = n_core)
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+disease_loo_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +elpd_diff + +se_diff + +elpd_loo + +se_elpd_loo + +p_loo + +se_p_loo + +looic + +se_looic +
+adjusted_type_specific_negbin + +0.00000 + +0.00000 + +-762.0105 + +24.36869 + +88.10476 + +5.429932 + +1524.021 + +48.73737 +
+adjusted_type_specific_poisson + +-15.25917 + +11.12194 + +-777.2696 + +29.14080 + +185.09482 + +13.573559 + +1554.539 + +58.28159 +
+type_specific_negbin + +-162.73225 + +12.55451 + +-924.7427 + +27.37412 + +57.63924 + +5.081431 + +1849.485 + +54.74825 +
+adjusted_null_negbin + +-201.65210 + +15.53140 + +-963.6626 + +29.65337 + +46.83912 + +6.993739 + +1927.325 + +59.30675 +
+null_negbin + +-253.69192 + +15.42140 + +-1015.7024 + +29.41430 + +24.12326 + +4.540623 + +2031.405 + +58.82859 +
+adjusted_null_poisson + +-815.04598 + +96.09333 + +-1577.0564 + +106.37968 + +551.73939 + +52.174102 + +3154.113 + +212.75936 +
+type_specific_poisson + +-825.44431 + +116.26527 + +-1587.4548 + +125.20208 + +604.47856 + +64.797459 + +3174.910 + +250.40416 +
+null_poisson + +-1741.04324 + +191.89450 + +-2503.0537 + +200.99005 + +896.02268 + +82.394407 + +5006.107 + +401.98010 +
+

+write.csv(disease_loo_comparison,
+          file = "child_disease_serotype_loo_comparison.csv",
+          quote = FALSE,
+          row.names = FALSE)

Run model comparison with Bayes factors

As the models can instead be compared with Bayes factors:

+

+bf_comparison <- 
+  progressionEstimation::compare_model_fits_with_bf(fit_list,
+                                                    num_iter = n_iter,
+                                                    num_threads = n_core)
+
+bf_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Model + +log_Bayes_factor +
+adjusted_type_specific_negbin + +0.00000 +
+adjusted_type_specific_poisson + +-30.91517 +
+type_specific_negbin + +-96.17864 +
+adjusted_null_negbin + +-119.46761 +
+null_negbin + +-142.09530 +
+adjusted_null_poisson + +-793.66042 +
+type_specific_poisson + +-840.98152 +
+null_poisson + +-1838.49370 +
+

+write.csv(bf_comparison,
+          file = "child_disease_serotype_bf_comparison.csv",
+          quote = FALSE,
+          row.names = FALSE)

Plot serotype invasiveness

The best-fitting model can then be applied to the overall dataset.

-

-full_infant_serotype_invasiveness <- 
-  progressionEstimation::process_input_data(
-    S_pneumoniae_infant_serotype %<>%
-      dplyr::mutate(study = factor(study, levels = studies_by_size)
-      )
-    )
-
-full_adjusted_type_specific_poisson_fit <- 
-  progressionEstimation::fit_progression_rate_model(full_infant_serotype_invasiveness,
-                                                    type_specific = TRUE,
-                                                    location_adjustment = TRUE,
-                                                    stat_model = "poisson",
-                                                    num_chains = n_chains,
-                                                    num_iter = n_iter,
-                                                    num_cores = n_core)
-
-rhat_plot <- plot(full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005)
-
-trace_plot <- rstan::traceplot(full_adjusted_type_specific_poisson_fit, pars = "lp__") +
-                theme(axis.text.x = element_text(angle = 90))
-
-best_fitting_model_validation_plot <- cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
-                   nrow = 1,
-                   ncol = 2,
-                   labels = "AUTO")
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-ggsave(best_fitting_model_validation_plot,
-       file = "best_fitting_infant_model_validation_plot.png",
-       width = 8,
-       height = 6)
-

-mixedrank = function(x) order(gtools::mixedorder(as.character(x)))
-
-# Annotate serotypes by status
-best_fitting_output <- 
-  progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_poisson_fit,
-                                                               S_pneumoniae_infant_serotype) %>%
-    dplyr::mutate("classification" = dplyr::case_when(
-        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
-        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
-        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
-        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
-        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
-        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
-        TRUE ~ "No PCV"
-      )
-    ) %>%
-    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
-                                                                     "PCV10",
-                                                                     "PCV13",
-                                                                     "PCV15",
-                                                                     "PCV20",
-                                                                     "PPV23",
-                                                                     "No PCV")))
-
-# Order serotypes
-serotype_levels <-
-  best_fitting_output %>%
-    dplyr::select(type,classification) %>%
-    dplyr::distinct() %>%
-    group_by(classification) %>%
-    dplyr::arrange(mixedrank(type),
-                   .by_group = TRUE) %>%
-    ungroup() %>%
-    dplyr::select(type) %>%
-    dplyr::pull()
-
-best_fitting_output %<>%
-  dplyr::mutate(type = factor(type, levels = serotype_levels))
-
-# Plot
-(invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(best_fitting_output,
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE))
-

-

-ggsave(invasiveness_plot,
-       file = "full_serotype_invasiveness_plot.png",
-       height = 8,
-       width = 8)
-
-write.csv(best_fitting_output,
-          file = "study_adjusted_type_specific_poisson_serotype_fit.csv",
-          quote = F,
-          row.names = F)
-
-write.csv(best_fitting_output %>%
-            dplyr::select(type,nu,nu_lower,nu_upper) %>%
-            dplyr::rename(invasiveness = nu) %>%
-            dplyr::rename(invasiveness_lower = nu_lower) %>%
-            dplyr::rename(invasiveness_upper = nu_upper) %>%
-            dplyr::distinct(),
-          file = "Dataset_S1.csv",
-          quote = F,
-          row.names = F)
+

+full_infant_serotype_invasiveness <- 
+  progressionEstimation::process_input_data(
+    S_pneumoniae_infant_serotype %<>%
+      dplyr::mutate(study = factor(study, levels = studies_by_size)
+      )
+    )
+
+full_adjusted_type_specific_negbin_fit <- 
+  progressionEstimation::fit_progression_rate_model(full_infant_serotype_invasiveness,
+                                                    type_specific = TRUE,
+                                                    location_adjustment = TRUE,
+                                                    stat_model = "negbin",
+                                                    num_chains = n_chains,
+                                                    num_iter = n_iter,
+                                                    num_cores = n_core)
+
+rhat_plot <- plot(full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005)
+
+trace_plot <- rstan::traceplot(full_adjusted_type_specific_negbin_fit, pars = "lp__") +
+                theme(axis.text.x = element_text(angle = 90))
+
+best_fitting_model_validation_plot <- cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
+                   nrow = 1,
+                   ncol = 2,
+                   labels = "AUTO")
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+ggsave(best_fitting_model_validation_plot,
+       file = "best_fitting_infant_model_validation_plot.pdf",
+       width = 8,
+       height = 6)
+

+mixedrank = function(x) order(gtools::mixedorder(as.character(x)))
+
+# Annotate serotypes by status
+best_fitting_output <- 
+  progressionEstimation::process_progression_rate_model_output(full_adjusted_type_specific_negbin_fit,
+                                                               S_pneumoniae_infant_serotype) %>%
+    dplyr::mutate("classification" = dplyr::case_when(
+        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
+        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
+        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
+        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
+        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
+        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
+        TRUE ~ "No PCV"
+      )
+    ) %>%
+    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                     "PCV10",
+                                                                     "PCV13",
+                                                                     "PCV15",
+                                                                     "PCV20",
+                                                                     "PPV23",
+                                                                     "No PCV")))
+
+# Order serotypes
+serotype_levels <-
+  best_fitting_output %>%
+    dplyr::select(type,classification) %>%
+    dplyr::distinct() %>%
+    group_by(classification) %>%
+    dplyr::arrange(mixedrank(type),
+                   .by_group = TRUE) %>%
+    ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::pull()
+
+best_fitting_output %<>%
+  dplyr::mutate(type = factor(type, levels = serotype_levels))
+
+# Plot
+(invasiveness_plot <-
+  progressionEstimation::plot_progression_rates(best_fitting_output,
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE))
+

+

+ggsave(invasiveness_plot,
+       file = "full_serotype_invasiveness_plot.pdf",
+       height = 8,
+       width = 8)
+
+write.csv(best_fitting_output,
+          file = "study_adjusted_type_specific_negbin_serotype_fit.csv",
+          quote = F,
+          row.names = F)
+
+write.csv(best_fitting_output %>%
+            dplyr::select(type,nu,nu_lower,nu_upper) %>%
+            dplyr::rename(invasiveness = nu) %>%
+            dplyr::rename(invasiveness_lower = nu_lower) %>%
+            dplyr::rename(invasiveness_upper = nu_upper) %>%
+            dplyr::distinct(),
+          file = "Dataset_S1.csv",
+          quote = F,
+          row.names = F)

Plot study-specific scale factors

-

-(scale_factor_plot <-
-  progressionEstimation::plot_study_scale_factors(best_fitting_output))
-

+

+(scale_factor_plot <-
+  progressionEstimation::plot_study_scale_factors(best_fitting_output))
+

Compare a model fit that account for PCVs protecting against disease

If PCVs provide further protection against disease, relative to carriage, then their invasiveness may reduce post-PCV. Therefore we can treat them as different serotypes pre- and post-PCV.

-

-pv_S_pneumoniae_infant_serotype <-
-  S_pneumoniae_infant_serotype %>%
-    dplyr::mutate(type = dplyr::case_when(
-                      type %in% vaccine_types[["PCV7"]] & grepl("post.PCV", study) ~ paste0(type,"_pv"),
-                      type == "6A" & grepl("post.PCV", study) ~ paste0(type,"_pv"),
-                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV10", study) ~ paste0(type,"_pv"),
-                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
-                      type %in% vaccine_types[["PCV13"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
-                      type == "6C" & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
-                      TRUE ~ as.character(type)
-                    )
-                  ) %>%
-  dplyr::mutate(type = factor(type))
-
-pv_S_pneumoniae_infant_serotype %<>%
-  dplyr::mutate(study = factor(study, levels = studies_by_size))
-
-pv_full_infant_serotype_invasiveness <- 
-  progressionEstimation::process_input_data(pv_S_pneumoniae_infant_serotype)
-
-pv_full_adjusted_type_specific_poisson_fit <- 
-  progressionEstimation::fit_progression_rate_model(pv_full_infant_serotype_invasiveness,
-                                                    type_specific = TRUE,
-                                                    location_adjustment = TRUE,
-                                                    stat_model = "poisson",
-                                                    num_chains = n_chains,
-                                                    num_iter = n_iter,
-                                                    num_cores = n_core)
-
-rhat_plot <- plot(pv_full_adjusted_type_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005)
-
-trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_poisson_fit, pars = "lp__") +
-                theme(axis.text.x = element_text(angle = 90, size = 8))
-
-best_fitting_pv_model_validation_plot <- 
-  cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
-                   nrow = 1,
-                   ncol = 2,
-                   labels = "AUTO")
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-ggsave(best_fitting_pv_model_validation_plot,
-       file = "best_fitting_pv_infant_model_validation_plot.png",
-       width = 8,
-       height = 6)
-

-pv_best_fitting_output <- 
-  progressionEstimation::process_progression_rate_model_output(
-    pv_full_adjusted_type_specific_poisson_fit,                                                 pv_S_pneumoniae_infant_serotype) %>%
-      dplyr::mutate("classification" = dplyr::case_when(
-          gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7",
-          gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10",
-          gsub("_pv","",type) %in% vaccine_types[["PCV13"]] ~ "PCV13",
-          gsub("_pv","",type) %in% vaccine_types[["PCV15"]] ~ "PCV15",
-          gsub("_pv","",type) %in% vaccine_types[["PCV20"]] ~ "PCV20",
-          gsub("_pv","",type) %in% vaccine_types[["PPV23"]] ~ "PPV23",
-          TRUE ~ "No PCV"
-        )
-      ) %>%
-      dplyr::mutate(classification = factor(classification, levels = c("PCV7",
-                                                                       "PCV10",
-                                                                       "PCV13",
-                                                                       "PCV15",
-                                                                       "PCV20",
-                                                                       "PPV23",
-                                                                       "No PCV")))
-
-# Order serotypes
-pv_serotype_levels <-
-  pv_best_fitting_output %>%
-    dplyr::select(type,classification) %>%
-    dplyr::distinct() %>%
-    group_by(classification) %>%
-    dplyr::arrange(mixedrank(type),
-                   .by_group = TRUE) %>%
-    ungroup() %>%
-    dplyr::select(type) %>%
-    dplyr::pull()
-
-pv_best_fitting_output %<>%
-  dplyr::mutate(type = factor(type, levels = pv_serotype_levels))
-
-# Plot
-(pv_invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(pv_best_fitting_output,
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE))
-

-

-(joint_invasiveness_plot <-
-    cowplot::plot_grid(plotlist = list(invasiveness_plot + theme(legend.position = "none"), pv_invasiveness_plot),
-                       nrow = 2,
-                       ncol = 1,
-                       rel_heights = c(1,1.2),
-                       labels = "AUTO"
-                       )
-)
-

-

-ggsave(joint_invasiveness_plot,
-       file = "joint_infant_serotype_plot.png",
-       height = 10,
-       width = 9)
-

-(pv_scale_factor_plot <-
-  progressionEstimation::plot_study_scale_factors(pv_best_fitting_output))
-

+

+pv_S_pneumoniae_infant_serotype <-
+  S_pneumoniae_infant_serotype %>%
+    dplyr::mutate(type = dplyr::case_when(
+                      type %in% vaccine_types[["PCV7"]] & grepl("post.PCV", study) ~ paste0(type,"_pv"),
+                      type == "6A" & grepl("post.PCV", study) ~ paste0(type,"_pv"),
+                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV10", study) ~ paste0(type,"_pv"),
+                      type %in% vaccine_types[["PCV10"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
+                      type %in% vaccine_types[["PCV13"]] & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
+                      type == "6C" & grepl("post.PCV13", study) ~ paste0(type,"_pv"),
+                      TRUE ~ as.character(type)
+                    )
+                  ) %>%
+  dplyr::mutate(type = factor(type))
+
+pv_S_pneumoniae_infant_serotype %<>%
+  dplyr::mutate(study = factor(study, levels = studies_by_size))
+
+pv_full_infant_serotype_invasiveness <- 
+  progressionEstimation::process_input_data(pv_S_pneumoniae_infant_serotype)
+
+pv_full_adjusted_type_specific_negbin_fit <- 
+  progressionEstimation::fit_progression_rate_model(pv_full_infant_serotype_invasiveness,
+                                                    type_specific = TRUE,
+                                                    location_adjustment = TRUE,
+                                                    stat_model = "negbin",
+                                                    num_chains = n_chains,
+                                                    num_iter = n_iter,
+                                                    num_cores = n_core)
+
+rhat_plot <- plot(pv_full_adjusted_type_specific_negbin_fit, plotfun = "rhat", binwidth = 0.00005)
+
+trace_plot <- rstan::traceplot(pv_full_adjusted_type_specific_negbin_fit, pars = "lp__") +
+                theme(axis.text.x = element_text(angle = 90, size = 8))
+
+best_fitting_pv_model_validation_plot <- 
+  cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
+                   nrow = 1,
+                   ncol = 2,
+                   labels = "AUTO")
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+ggsave(best_fitting_pv_model_validation_plot,
+       file = "best_fitting_pv_infant_model_validation_plot.pdf",
+       width = 8,
+       height = 6)
+

+pv_best_fitting_output <- 
+  progressionEstimation::process_progression_rate_model_output(
+    pv_full_adjusted_type_specific_negbin_fit,                                                 pv_S_pneumoniae_infant_serotype) %>%
+      dplyr::mutate("classification" = dplyr::case_when(
+          gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7",
+          gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10",
+          gsub("_pv","",type) %in% vaccine_types[["PCV13"]] ~ "PCV13",
+          gsub("_pv","",type) %in% vaccine_types[["PCV15"]] ~ "PCV15",
+          gsub("_pv","",type) %in% vaccine_types[["PCV20"]] ~ "PCV20",
+          gsub("_pv","",type) %in% vaccine_types[["PPV23"]] ~ "PPV23",
+          TRUE ~ "No PCV"
+        )
+      ) %>%
+      dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                       "PCV10",
+                                                                       "PCV13",
+                                                                       "PCV15",
+                                                                       "PCV20",
+                                                                       "PPV23",
+                                                                       "No PCV")))
+
+# Order serotypes
+pv_serotype_levels <-
+  pv_best_fitting_output %>%
+    dplyr::select(type,classification) %>%
+    dplyr::distinct() %>%
+    group_by(classification) %>%
+    dplyr::arrange(mixedrank(type),
+                   .by_group = TRUE) %>%
+    ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::pull()
+
+pv_best_fitting_output %<>%
+  dplyr::mutate(type = factor(type, levels = pv_serotype_levels))
+
+# Plot
+(pv_invasiveness_plot <-
+  progressionEstimation::plot_progression_rates(pv_best_fitting_output,
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE))
+

+

+(joint_invasiveness_plot <-
+    cowplot::plot_grid(plotlist = list(invasiveness_plot + theme(legend.position = "none"), pv_invasiveness_plot),
+                       nrow = 2,
+                       ncol = 1,
+                       rel_heights = c(1,1.2),
+                       labels = "AUTO"
+                       )
+)
+

+

+ggsave(joint_invasiveness_plot,
+       file = "joint_infant_serotype_plot.pdf",
+       height = 10,
+       width = 9)
+

+(pv_scale_factor_plot <-
+  progressionEstimation::plot_study_scale_factors(pv_best_fitting_output))
+

Comparison with odds ratio calculation

-

-require(ggpubr)
-#> Loading required package: ggpubr
-#> 
-#> Attaching package: 'ggpubr'
-#> The following object is masked from 'package:cowplot':
-#> 
-#>     get_legend
-require(metafor)
-#> Loading required package: metafor
-#> Loading required package: Matrix
-#> 
-#> Attaching package: 'Matrix'
-#> The following objects are masked from 'package:tidyr':
-#> 
-#>     expand, pack, unpack
-#> 
-#> Loading the 'metafor' package (version 3.0-2). For an
-#> introduction to the package please type: help(metafor)
-
-get_serotype_stats <- function(serotype, df) {
-  sero_df <-
-    df %>%
-      tidyr::pivot_longer(c(carriage,disease),
-                          names_to = "clinical_manifestation",
-                          values_to = "observation") %>%
-      dplyr::group_by(study) %>%
-      dplyr::mutate(matching_type = dplyr::if_else(type == serotype,1,0)) %>%
-      dplyr::mutate(matching_type_disease =
-                      sum(observation[clinical_manifestation == "disease" & matching_type == 1])) %>%
-      dplyr::mutate(matching_type_carriage =
-                      sum(observation[clinical_manifestation == "carriage" & matching_type == 1])) %>%
-      dplyr::mutate(non_matching_type_disease =
-                      sum(observation[clinical_manifestation == "disease" & matching_type == 0])) %>%
-      dplyr::mutate(non_matching_type_carriage =
-                      sum(observation[clinical_manifestation == "carriage" & matching_type == 0])) %>%
-      dplyr::ungroup() %>%
-    dplyr::select(study,matching_type_disease,matching_type_carriage,non_matching_type_disease,non_matching_type_carriage) %>%
-    dplyr::distinct() %>%
-    dplyr::mutate(serotype = serotype) %>%
-    dplyr::filter(matching_type_carriage > 0 | matching_type_disease > 0)
-  return(sero_df)
-}
-
-per_serotype_estimate <- function(test_serotype, df, method_type = "FE") {
-  per_serotype_out <- metafor::rma(yi = yi,
-                                   vi = vi,
-                                   data = df,
-                                   slab = study,
-                                   subset = serotype == test_serotype,
-                                   method = method_type,
-                                   control=list(stepadj=0.5, maxiter=10000))
-  summary_df <-
-    data.frame(
-      "Analysis" = method_type,
-      "Serotype" = test_serotype,
-      "OR" = as.numeric(per_serotype_out$b),
-      "OR_upper" = per_serotype_out$ci.ub,
-      "OR_lower" = per_serotype_out$ci.lb,
-      "tau_squared" = per_serotype_out$tau2,
-      "i_squared" = per_serotype_out$I2,
-      "h_squared" = per_serotype_out$H2
-    )
-  return(summary_df)
-}
-
-serotype_or_df <- dplyr::bind_rows(lapply(
-                                   serotype_levels,
-                                   get_serotype_stats,
-                                   S_pneumoniae_infant_serotype)
-)
-
-serotype_effect_size_df <- metafor::escalc(measure = "OR",
-                                            ai = matching_type_disease,
-                                            bi = matching_type_carriage,
-                                            ci = non_matching_type_disease,
-                                            di = non_matching_type_carriage,
-                                            slab = study,
-                                            data = serotype_or_df)
-
-per_serotype_out <- dplyr::bind_rows(
-                    lapply(
-                      serotype_levels,
-                      per_serotype_estimate,
-                      serotype_effect_size_df
-                    ),
-                    lapply(
-                      serotype_levels,
-                      per_serotype_estimate,
-                      serotype_effect_size_df,
-                      method_type = "REML"
-                    )
-)
-
-sample_sizes <-
-  best_fitting_output %>%
-      dplyr::group_by(type) %>%
-      dplyr::mutate(num_samples = sum(carriage+disease)) %>%
-      dplyr::mutate(Sample_count = dplyr::case_when(
-                        num_samples < 11 ~ "0-10",
-                        num_samples < 51 ~ "11-50",
-                        num_samples < 101 ~ "51-100",
-                        TRUE ~ ">100"
-                      )
-                    ) %>%
-      dplyr::ungroup() %>%
-      dplyr::select(type, Sample_count) %>%
-      dplyr::distinct() %>%
-      dplyr::mutate(Sample_count = factor(Sample_count,
-                                          levels = c("0-10",
-                                                     "11-50",
-                                                     "51-100",
-                                                     ">100")))
-
-# Combine the invasiveness estimates
-combined_invasiveness_df <-
-  dplyr::bind_rows(
-    per_serotype_out %>%
-      dplyr::select(Analysis, Serotype, OR, OR_upper, OR_lower) %>%
-      dplyr::rename(Invasiveness = OR) %>%
-      dplyr::rename(Invasiveness_upper = OR_upper) %>%
-      dplyr::rename(Invasiveness_lower = OR_lower),
-    best_fitting_output %>%
-      dplyr::select(model_name, nu, nu_lower, nu_upper, type) %>%
-      dplyr::distinct() %>%
-      dplyr::rename(Analysis = model_name) %>%
-      dplyr::rename(Serotype = type) %>%
-      dplyr::rename(Invasiveness = nu) %>%
-      dplyr::rename(Invasiveness_upper = nu_upper) %>%
-      dplyr::rename(Invasiveness_lower = nu_lower)
-  ) %>%
-  tidyr::pivot_wider(id_cols = Serotype,
-                     names_from = Analysis,
-                     values_from = c(Invasiveness,Invasiveness_upper,Invasiveness_lower),
-                     names_sep = "_") %>%
-    dplyr::mutate("classification" = dplyr::case_when(
-        Serotype %in% vaccine_types[["PCV7"]] ~ "PCV7",
-        Serotype %in% vaccine_types[["PCV10"]] ~ "PCV10",
-        Serotype %in% vaccine_types[["PCV13"]] ~ "PCV13",
-        Serotype %in% vaccine_types[["PCV15"]] ~ "PCV15",
-        Serotype %in% vaccine_types[["PCV20"]] ~ "PCV20",
-        Serotype %in% vaccine_types[["PPV23"]] ~ "PPV23",
-        TRUE ~ "No PCV"
-      )
-    ) %>%
-  dplyr::left_join(sample_sizes, by = c("Serotype" = "type"))
-
-# Plot comparison of invasiveness estimates
-(fixed_effects_comparison <-
-  ggplot(combined_invasiveness_df,
-       aes(x = Invasiveness_adjusted_type_specific_poisson,
-           xmin = Invasiveness_lower_adjusted_type_specific_poisson,
-           xmax = Invasiveness_upper_adjusted_type_specific_poisson,
-           y = Invasiveness_FE,
-           ymin = Invasiveness_lower_FE,
-           ymax = Invasiveness_upper_FE,
-           colour = classification)) +
-  geom_errorbar(alpha = 0.25) +
-  geom_errorbarh(alpha = 0.25) +
-  geom_point() +
-  scale_x_continuous(trans = "log10") +
-  theme_bw() +
-  scale_color_manual(values = vaccine_colours) +
-  theme(legend.position = "bottom") +
-  ylab("Invasiveness estimated from log odds ratio") +
-  xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") +
-  facet_wrap(~Sample_count) +
-  stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson,
-               y = Invasiveness_FE),
-           inherit.aes = FALSE,
-           method = "kendall",
-           cor.coef.name = "tau") +
-  ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
-                                    dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
-                            aes(label = Serotype)
-                            )
-)
-

-

-# Plot comparison of invasiveness estimates
-(random_effects_comparison <-
-  ggplot(combined_invasiveness_df,
-         aes(x = Invasiveness_adjusted_type_specific_poisson,
-             xmin = Invasiveness_lower_adjusted_type_specific_poisson,
-             xmax = Invasiveness_upper_adjusted_type_specific_poisson,
-             y = Invasiveness_REML,
-             ymin = Invasiveness_lower_REML,
-             ymax = Invasiveness_upper_REML,
-             colour = classification)) +
-    geom_errorbar(alpha = 0.25) +
-    geom_errorbarh(alpha = 0.25) +
-    geom_point() +
-    scale_x_continuous(trans = "log10") +
-    theme_bw() +
-    scale_color_manual(values = vaccine_colours) +
-    theme(legend.position = "bottom") +
-    ylab("Invasiveness estimated from log odds ratio") +
-    xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") +
-    facet_wrap(~Sample_count) +
-    stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson,
-                 y = Invasiveness_REML),
-             inherit.aes = FALSE,
-             method = "kendall",
-             cor.coef.name = "tau") +
-    ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
-                                      dplyr::filter((Invasiveness_adjusted_type_specific_poisson < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
-                              aes(label = Serotype)
-                              )
-)
-

-

-combined_odds_ratio_plot <-
-  cowplot::plot_grid(
-    plotlist = list(fixed_effects_comparison + theme(legend.position = "none"),
-                    random_effects_comparison),
-    ncol = 1,
-    nrow = 2,
-    rel_heights = c(1,1.2),
-    labels = "AUTO"
-  )
-
-ggsave(combined_odds_ratio_plot,
-       file = "combined_odds_ratio_plot.png",
-       width = 8,
-       height = 12)
+

+require(ggpubr)
+#> Loading required package: ggpubr
+#> 
+#> Attaching package: 'ggpubr'
+#> The following object is masked from 'package:cowplot':
+#> 
+#>     get_legend
+require(metafor)
+#> Loading required package: metafor
+#> Loading required package: Matrix
+#> 
+#> Attaching package: 'Matrix'
+#> The following objects are masked from 'package:tidyr':
+#> 
+#>     expand, pack, unpack
+#> 
+#> Loading the 'metafor' package (version 3.0-2). For an
+#> introduction to the package please type: help(metafor)
+
+get_serotype_stats <- function(serotype, df) {
+  sero_df <-
+    df %>%
+      tidyr::pivot_longer(c(carriage,disease),
+                          names_to = "clinical_manifestation",
+                          values_to = "observation") %>%
+      dplyr::group_by(study) %>%
+      dplyr::mutate(matching_type = dplyr::if_else(type == serotype,1,0)) %>%
+      dplyr::mutate(matching_type_disease =
+                      sum(observation[clinical_manifestation == "disease" & matching_type == 1])) %>%
+      dplyr::mutate(matching_type_carriage =
+                      sum(observation[clinical_manifestation == "carriage" & matching_type == 1])) %>%
+      dplyr::mutate(non_matching_type_disease =
+                      sum(observation[clinical_manifestation == "disease" & matching_type == 0])) %>%
+      dplyr::mutate(non_matching_type_carriage =
+                      sum(observation[clinical_manifestation == "carriage" & matching_type == 0])) %>%
+      dplyr::ungroup() %>%
+    dplyr::select(study,matching_type_disease,matching_type_carriage,non_matching_type_disease,non_matching_type_carriage) %>%
+    dplyr::distinct() %>%
+    dplyr::mutate(serotype = serotype) %>%
+    dplyr::filter(matching_type_carriage > 0 | matching_type_disease > 0)
+  return(sero_df)
+}
+
+per_serotype_estimate <- function(test_serotype, df, method_type = "FE") {
+  per_serotype_out <- metafor::rma(yi = yi,
+                                   vi = vi,
+                                   data = df,
+                                   slab = study,
+                                   subset = serotype == test_serotype,
+                                   method = method_type,
+                                   control=list(stepadj=0.5, maxiter=10000))
+  summary_df <-
+    data.frame(
+      "Analysis" = method_type,
+      "Serotype" = test_serotype,
+      "OR" = as.numeric(per_serotype_out$b),
+      "OR_upper" = per_serotype_out$ci.ub,
+      "OR_lower" = per_serotype_out$ci.lb,
+      "tau_squared" = per_serotype_out$tau2,
+      "i_squared" = per_serotype_out$I2,
+      "h_squared" = per_serotype_out$H2
+    )
+  return(summary_df)
+}
+
+serotype_or_df <- dplyr::bind_rows(lapply(
+                                   serotype_levels,
+                                   get_serotype_stats,
+                                   S_pneumoniae_infant_serotype)
+)
+
+serotype_effect_size_df <- metafor::escalc(measure = "OR",
+                                            ai = matching_type_disease,
+                                            bi = matching_type_carriage,
+                                            ci = non_matching_type_disease,
+                                            di = non_matching_type_carriage,
+                                            slab = study,
+                                            data = serotype_or_df)
+
+per_serotype_out <- dplyr::bind_rows(
+                    lapply(
+                      serotype_levels,
+                      per_serotype_estimate,
+                      serotype_effect_size_df
+                    ),
+                    lapply(
+                      serotype_levels,
+                      per_serotype_estimate,
+                      serotype_effect_size_df,
+                      method_type = "REML"
+                    )
+)
+
+sample_sizes <-
+  best_fitting_output %>%
+      dplyr::group_by(type) %>%
+      dplyr::mutate(num_samples = sum(carriage+disease)) %>%
+      dplyr::mutate(Sample_count = dplyr::case_when(
+                        num_samples < 11 ~ "0-10",
+                        num_samples < 51 ~ "11-50",
+                        num_samples < 101 ~ "51-100",
+                        TRUE ~ ">100"
+                      )
+                    ) %>%
+      dplyr::ungroup() %>%
+      dplyr::select(type, Sample_count) %>%
+      dplyr::distinct() %>%
+      dplyr::mutate(Sample_count = factor(Sample_count,
+                                          levels = c("0-10",
+                                                     "11-50",
+                                                     "51-100",
+                                                     ">100")))
+
+# Combine the invasiveness estimates
+combined_invasiveness_df <-
+  dplyr::bind_rows(
+    per_serotype_out %>%
+      dplyr::select(Analysis, Serotype, OR, OR_upper, OR_lower) %>%
+      dplyr::rename(Invasiveness = OR) %>%
+      dplyr::rename(Invasiveness_upper = OR_upper) %>%
+      dplyr::rename(Invasiveness_lower = OR_lower),
+    best_fitting_output %>%
+      dplyr::select(model_name, nu, nu_lower, nu_upper, type) %>%
+      dplyr::distinct() %>%
+      dplyr::rename(Analysis = model_name) %>%
+      dplyr::rename(Serotype = type) %>%
+      dplyr::rename(Invasiveness = nu) %>%
+      dplyr::rename(Invasiveness_upper = nu_upper) %>%
+      dplyr::rename(Invasiveness_lower = nu_lower)
+  ) %>%
+  tidyr::pivot_wider(id_cols = Serotype,
+                     names_from = Analysis,
+                     values_from = c(Invasiveness,Invasiveness_upper,Invasiveness_lower),
+                     names_sep = "_") %>%
+    dplyr::mutate("classification" = dplyr::case_when(
+        Serotype %in% vaccine_types[["PCV7"]] ~ "PCV7",
+        Serotype %in% vaccine_types[["PCV10"]] ~ "PCV10",
+        Serotype %in% vaccine_types[["PCV13"]] ~ "PCV13",
+        Serotype %in% vaccine_types[["PCV15"]] ~ "PCV15",
+        Serotype %in% vaccine_types[["PCV20"]] ~ "PCV20",
+        Serotype %in% vaccine_types[["PPV23"]] ~ "PPV23",
+        TRUE ~ "No PCV"
+      )
+    ) %>%
+  dplyr::left_join(sample_sizes, by = c("Serotype" = "type"))
+
+# Plot comparison of invasiveness estimates
+(fixed_effects_comparison <-
+  ggplot(combined_invasiveness_df,
+       aes(x = Invasiveness_adjusted_type_specific_negbin,
+           xmin = Invasiveness_lower_adjusted_type_specific_negbin,
+           xmax = Invasiveness_upper_adjusted_type_specific_negbin,
+           y = Invasiveness_FE,
+           ymin = Invasiveness_lower_FE,
+           ymax = Invasiveness_upper_FE,
+           colour = classification)) +
+  geom_errorbar(alpha = 0.25) +
+  geom_errorbarh(alpha = 0.25) +
+  geom_point() +
+  scale_x_continuous(trans = "log10") +
+  theme_bw() +
+  scale_color_manual(values = vaccine_colours) +
+  theme(legend.position = "bottom") +
+  ylab("Invasiveness estimated from log odds ratio") +
+  xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") +
+  facet_wrap(~Sample_count) +
+  stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin,
+               y = Invasiveness_FE),
+           inherit.aes = FALSE,
+           method = "kendall",
+           cor.coef.name = "tau") +
+  ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
+                                    dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
+                            aes(label = Serotype)
+                            )
+)
+#> Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider
+#> increasing max.overlaps
+

+

+# Plot comparison of invasiveness estimates
+(random_effects_comparison <-
+  ggplot(combined_invasiveness_df,
+         aes(x = Invasiveness_adjusted_type_specific_negbin,
+             xmin = Invasiveness_lower_adjusted_type_specific_negbin,
+             xmax = Invasiveness_upper_adjusted_type_specific_negbin,
+             y = Invasiveness_REML,
+             ymin = Invasiveness_lower_REML,
+             ymax = Invasiveness_upper_REML,
+             colour = classification)) +
+    geom_errorbar(alpha = 0.25) +
+    geom_errorbarh(alpha = 0.25) +
+    geom_point() +
+    scale_x_continuous(trans = "log10") +
+    theme_bw() +
+    scale_color_manual(values = vaccine_colours) +
+    theme(legend.position = "bottom") +
+    ylab("Invasiveness estimated from log odds ratio") +
+    xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") +
+    facet_wrap(~Sample_count) +
+    stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin,
+                 y = Invasiveness_REML),
+             inherit.aes = FALSE,
+             method = "kendall",
+             cor.coef.name = "tau") +
+    ggrepel::geom_label_repel(data = combined_invasiveness_df %>%
+                                      dplyr::filter((Invasiveness_adjusted_type_specific_negbin < 0.0005 & Invasiveness_FE > 0) | Serotype == "46"),
+                              aes(label = Serotype)
+                              )
+)
+#> Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider
+#> increasing max.overlaps
+

+

+combined_odds_ratio_plot <-
+  cowplot::plot_grid(
+    plotlist = list(fixed_effects_comparison + theme(legend.position = "none"),
+                    random_effects_comparison),
+    ncol = 1,
+    nrow = 2,
+    rel_heights = c(1,1.2),
+    labels = "AUTO"
+  )
+
+ggsave(combined_odds_ratio_plot,
+       file = "combined_odds_ratio_plot.pdf",
+       width = 8,
+       height = 12)
+#> Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
+#> increasing max.overlaps
+#> Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
+#> increasing max.overlaps

This comparison can be extended to location-specific invasiveness factors, which incorporate the uncertainty of the study-specific adjustment factor:

-

-netherland_pre_pcv_invasiveness_df <-
-  progressionEstimation::get_type_invasiveness_for_study(S_pneumoniae_infant_serotype,
-                         full_adjusted_type_specific_poisson_fit,
-                         study = "Netherlands.post.PCV10")
-
- netherland_pre_pcv_invasiveness_df %<>%
-      dplyr::mutate("classification" = dplyr::case_when(
-          gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7",
-          gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10",
-          gsub("_pv","",type) %in% vaccine_types[["PCV13"]] ~ "PCV13",
-          gsub("_pv","",type) %in% vaccine_types[["PCV15"]] ~ "PCV15",
-          gsub("_pv","",type) %in% vaccine_types[["PCV20"]] ~ "PCV20",
-          gsub("_pv","",type) %in% vaccine_types[["PPV23"]] ~ "PPV23",
-          TRUE ~ "No PCV"
-        )
-      ) %>%
-      dplyr::mutate(classification = factor(classification, levels = c("PCV7",
-                                                                       "PCV10",
-                                                                       "PCV13",
-                                                                       "PCV15",
-                                                                       "PCV20",
-                                                                       "PPV23",
-                                                                       "No PCV")))
-
-# Order serotypes
-serotype_levels <-
-  netherland_pre_pcv_invasiveness_df %>%
-    dplyr::select(type,classification) %>%
-    dplyr::distinct() %>%
-    group_by(classification) %>%
-    dplyr::arrange(mixedrank(type),
-                   .by_group = TRUE) %>%
-    ungroup() %>%
-    dplyr::select(type) %>%
-    dplyr::pull()
-
-netherland_pre_pcv_invasiveness_df %<>%
-  dplyr::mutate(type = factor(type, levels = serotype_levels))
-
-# Plot
-(netherlands_invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(netherland_pre_pcv_invasiveness_df,
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE))
-

+

+netherland_pre_pcv_invasiveness_df <-
+  progressionEstimation::get_type_invasiveness_for_study(S_pneumoniae_infant_serotype,
+                         full_adjusted_type_specific_negbin_fit,
+                         study = "Netherlands.post.PCV10")
+
+ netherland_pre_pcv_invasiveness_df %<>%
+      dplyr::mutate("classification" = dplyr::case_when(
+          gsub("_pv","",type) %in% vaccine_types[["PCV7"]] ~ "PCV7",
+          gsub("_pv","",type) %in% vaccine_types[["PCV10"]] ~ "PCV10",
+          gsub("_pv","",type) %in% vaccine_types[["PCV13"]] ~ "PCV13",
+          gsub("_pv","",type) %in% vaccine_types[["PCV15"]] ~ "PCV15",
+          gsub("_pv","",type) %in% vaccine_types[["PCV20"]] ~ "PCV20",
+          gsub("_pv","",type) %in% vaccine_types[["PPV23"]] ~ "PPV23",
+          TRUE ~ "No PCV"
+        )
+      ) %>%
+      dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                       "PCV10",
+                                                                       "PCV13",
+                                                                       "PCV15",
+                                                                       "PCV20",
+                                                                       "PPV23",
+                                                                       "No PCV")))
+
+# Order serotypes
+serotype_levels <-
+  netherland_pre_pcv_invasiveness_df %>%
+    dplyr::select(type,classification) %>%
+    dplyr::distinct() %>%
+    group_by(classification) %>%
+    dplyr::arrange(mixedrank(type),
+                   .by_group = TRUE) %>%
+    ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::pull()
+
+netherland_pre_pcv_invasiveness_df %<>%
+  dplyr::mutate(type = factor(type, levels = serotype_levels))
+
+# Plot
+(netherlands_invasiveness_plot <-
+  progressionEstimation::plot_progression_rates(netherland_pre_pcv_invasiveness_df,
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE))
+

This subset of serotypes can be compared with the odds ratios estimated using fixed effects:

-

-netherlands_or_comparison_df <-
-  netherland_pre_pcv_invasiveness_df %>%
-                       dplyr::rename(Serotype = type) %>%
-                       dplyr::rename(Netherlands_invasiveness = nu) %>%
-                       dplyr::rename(Netherlands_invasiveness_lower = nu_lower) %>%
-                       dplyr::rename(Netherlands_invasiveness_upper = nu_upper) %>%
-                       dplyr::select(-classification) %>%
-    dplyr::left_join(combined_invasiveness_df, by = c("Serotype"))
-
-# Plot comparison of invasiveness estimates
-(netherlands_fixed_or_comparison_plot <-
-  ggplot(netherlands_or_comparison_df,
-         aes(x = Netherlands_invasiveness,
-             xmin = Netherlands_invasiveness_lower,
-             xmax = Netherlands_invasiveness_upper,
-             y = Invasiveness_FE,
-             ymin = Invasiveness_lower_FE,
-             ymax = Invasiveness_upper_FE,
-             colour = classification)) +
-    geom_errorbar(alpha = 0.25) +
-    geom_errorbarh(alpha = 0.25) +
-    geom_point() +
-    scale_x_continuous(trans = "log10") +
-    theme_bw() +
-    scale_color_manual(values = vaccine_colours) +
-    theme(legend.position = "bottom") +
-    ylab("Invasiveness estimated from log odds ratio") +
-    xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") +
-    facet_wrap(~Sample_count) +
-    stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson,
-                 y = Invasiveness_FE),
-             inherit.aes = FALSE,
-             method = "kendall",
-             cor.coef.name = "tau")
-)
-

+

+netherlands_or_comparison_df <-
+  netherland_pre_pcv_invasiveness_df %>%
+                       dplyr::rename(Serotype = type) %>%
+                       dplyr::rename(Netherlands_invasiveness = nu) %>%
+                       dplyr::rename(Netherlands_invasiveness_lower = nu_lower) %>%
+                       dplyr::rename(Netherlands_invasiveness_upper = nu_upper) %>%
+                       dplyr::select(-classification) %>%
+    dplyr::left_join(combined_invasiveness_df, by = c("Serotype"))
+
+# Plot comparison of invasiveness estimates
+(netherlands_fixed_or_comparison_plot <-
+  ggplot(netherlands_or_comparison_df,
+         aes(x = Netherlands_invasiveness,
+             xmin = Netherlands_invasiveness_lower,
+             xmax = Netherlands_invasiveness_upper,
+             y = Invasiveness_FE,
+             ymin = Invasiveness_lower_FE,
+             ymax = Invasiveness_upper_FE,
+             colour = classification)) +
+    geom_errorbar(alpha = 0.25) +
+    geom_errorbarh(alpha = 0.25) +
+    geom_point() +
+    scale_x_continuous(trans = "log10") +
+    theme_bw() +
+    scale_color_manual(values = vaccine_colours) +
+    theme(legend.position = "bottom") +
+    ylab("Invasiveness estimated from log odds ratio") +
+    xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") +
+    facet_wrap(~Sample_count) +
+    stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin,
+                 y = Invasiveness_FE),
+             inherit.aes = FALSE,
+             method = "kendall",
+             cor.coef.name = "tau")
+)
+

The same comparison can be undertaken against odds ratios calculated with random effects:

-

-# Plot comparison of invasiveness estimates
-(netherlands_random_or_comparison_plot <-
-  ggplot(netherlands_or_comparison_df,
-         aes(x = Netherlands_invasiveness,
-             xmin = Netherlands_invasiveness_lower,
-             xmax = Netherlands_invasiveness_upper,
-             y = Invasiveness_REML,
-             ymin = Invasiveness_lower_REML,
-             ymax = Invasiveness_upper_REML,
-             colour = classification)) +
-    geom_errorbar(alpha = 0.25) +
-    geom_errorbarh(alpha = 0.25) +
-    geom_point() +
-    scale_x_continuous(trans = "log10") +
-    theme_bw() +
-    scale_color_manual(values = vaccine_colours) +
-    theme(legend.position = "bottom") +
-    ylab("Invasiveness estimated from log odds ratio") +
-    xlab("Invasivess estimate from adjusted type-specific Poisson (cases per carrier per year)") +
-    facet_wrap(~Sample_count) +
-    stat_cor(aes(x = Invasiveness_adjusted_type_specific_poisson,
-                 y = Invasiveness_REML),
-             inherit.aes = FALSE,
-             method = "kendall",
-             cor.coef.name = "tau")
-)
-

-

-combined_netherlands_or_comparison_plot <-
-  cowplot::plot_grid(plotlist = list(netherlands_fixed_or_comparison_plot,
-                                     netherlands_random_or_comparison_plot),
-                     nrow = 1,
-                     ncol = 2,
-                     labels = "AUTO")
-
-ggsave(combined_netherlands_or_comparison_plot,
-       file = "netherlands_or_comparison.png",
-       height = 8,
-       width = 14)
+

+# Plot comparison of invasiveness estimates
+(netherlands_random_or_comparison_plot <-
+  ggplot(netherlands_or_comparison_df,
+         aes(x = Netherlands_invasiveness,
+             xmin = Netherlands_invasiveness_lower,
+             xmax = Netherlands_invasiveness_upper,
+             y = Invasiveness_REML,
+             ymin = Invasiveness_lower_REML,
+             ymax = Invasiveness_upper_REML,
+             colour = classification)) +
+    geom_errorbar(alpha = 0.25) +
+    geom_errorbarh(alpha = 0.25) +
+    geom_point() +
+    scale_x_continuous(trans = "log10") +
+    theme_bw() +
+    scale_color_manual(values = vaccine_colours) +
+    theme(legend.position = "bottom") +
+    ylab("Invasiveness estimated from log odds ratio") +
+    xlab("Invasivess estimate from adjusted type-specific negative binomial (cases per carrier per year)") +
+    facet_wrap(~Sample_count) +
+    stat_cor(aes(x = Invasiveness_adjusted_type_specific_negbin,
+                 y = Invasiveness_REML),
+             inherit.aes = FALSE,
+             method = "kendall",
+             cor.coef.name = "tau")
+)
+

+

+combined_netherlands_or_comparison_plot <-
+  cowplot::plot_grid(plotlist = list(netherlands_fixed_or_comparison_plot,
+                                     netherlands_random_or_comparison_plot),
+                     nrow = 1,
+                     ncol = 2,
+                     labels = "AUTO")
+
+ggsave(combined_netherlands_or_comparison_plot,
+       file = "netherlands_or_comparison.pdf",
+       height = 8,
+       width = 14)

Comparison with carriage duration

-

-carriage_duration.df <- data.frame(
-  "type" = c("19F","23F","6B","14","21","19B","18C","29","3","4","24F","NT","5","6A","6C"),
-  "carriage_duration" = c(46.9,21,16.2,7.2,1.6,-0.1,-1.9,-4.3,-4.5,-7.2,-8.5,-12.3,-18.6,0,0)
-)
-
-carriage_duration.df %<>%
-  dplyr::inner_join(pv_best_fitting_output,
-                    by = "type") %>%
-  dplyr::select(type,carriage_duration,classification,nu,nu_lower,nu_upper) %>%
-  dplyr::distinct()
-
-(invasiveness_v_duration_plot <-
-  ggplot(carriage_duration.df,
-         aes(x = carriage_duration,
-             y = nu,
-             ymin = nu_lower,
-             ymax = nu_upper,
-             colour = classification)) +
-    geom_point() +
-    geom_errorbar() +
-    scale_colour_manual(values = vaccine_colours) +
-    ggrepel::geom_label_repel(aes(label = type)) +
-    scale_y_continuous(trans = "log10") +
-    ylab(expression(nu)) +
-    xlab("Carriage duration relative to serotype 6A/C") +
-    theme_bw()
-)
-

-

-ggsave(invasiveness_v_duration_plot,
-       file = "invasiveness_v_duration.png",
-       height = 8,
-       width = 8)
+

+carriage_duration.df <- data.frame(
+  "type" = c("19F","23F","6B","14","21","19B","18C","29","3","4","24F","NT","5","6A","6C"),
+  "carriage_duration" = c(46.9,21,16.2,7.2,1.6,-0.1,-1.9,-4.3,-4.5,-7.2,-8.5,-12.3,-18.6,0,0)
+)
+
+carriage_duration.df %<>%
+  dplyr::inner_join(pv_best_fitting_output,
+                    by = "type") %>%
+  dplyr::select(type,carriage_duration,classification,nu,nu_lower,nu_upper) %>%
+  dplyr::distinct()
+
+(invasiveness_v_duration_plot <-
+  ggplot(carriage_duration.df,
+         aes(x = carriage_duration,
+             y = nu,
+             ymin = nu_lower,
+             ymax = nu_upper,
+             colour = classification)) +
+    geom_point() +
+    geom_errorbar() +
+    scale_colour_manual(values = vaccine_colours) +
+    ggrepel::geom_label_repel(aes(label = type)) +
+    scale_y_continuous(trans = "log10") +
+    ylab(expression(nu)) +
+    xlab("Carriage duration relative to serotype 6A/C") +
+    theme_bw()
+)
+

+

+ggsave(invasiveness_v_duration_plot,
+       file = "invasiveness_v_duration.pdf",
+       height = 8,
+       width = 8)
diff --git a/examples/s-pneumoniae-strain-invasiveness-adults.Rmd b/examples/s-pneumoniae-strain-invasiveness-adults.Rmd index 91224ca..987aaa3 100644 --- a/examples/s-pneumoniae-strain-invasiveness-adults.Rmd +++ b/examples/s-pneumoniae-strain-invasiveness-adults.Rmd @@ -25,8 +25,120 @@ require(gtools) require(roxygen2) # Load stan package library(progressionEstimation) -pkgbuild::compile_dll() -roxygen2::roxygenize(package.dir = "..") +#pkgbuild::compile_dll() +#roxygen2::roxygenize(package.dir = "..") + +############# +# Functions # +############# + +plot_progression_rate_by_type <- function(model_output_df, + type = "type", + unit_time = "unit time", + type_name = "type", + colour_col = NULL, + colour_palette = NULL, + use_sample_size = FALSE) { + if (!(any(grepl("nu",colnames(model_output_df))))) { + stop("Need to include model output in data frame for plotting") + } + progression_rate_values <- c("nu", "nu_lower", "nu_upper") + if (type == "strain") { + progression_rate_values <- paste0("secondary_", progression_rate_values) + } + y_label_text = paste0("Progression rate contribution (disease per carrier per ",unit_time,")") + + model_output_df %<>% + dplyr::group_by(!!! dplyr::syms(type)) %>% + dplyr::mutate(num_observations = sum(carriage+disease)) %>% + dplyr::ungroup() + + if (type == "type") { + model_output_df %<>% + dplyr::group_by(!!! dplyr::syms(type),strain) %>% + dplyr::slice_head(n=1) %>% + dplyr::ungroup() + } else if (type == "strain") { + model_output_df %<>% + dplyr::group_by(!!! dplyr::syms(type),type) %>% + dplyr::slice_head(n=1) %>% + dplyr::ungroup() + } + + if (is.null(colour_col)) { + if (use_sample_size) { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]), + shape = num_observations)) + } else { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]))) + } + } else { + if (use_sample_size) { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]), + colour = get(colour_col), + fill = get(colour_col), + shape = num_observations)) + } else { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]), + colour = get(colour_col), + fill = get(colour_col))) + } + } + + point_graph <- + base_graph + + geom_point() + + geom_errorbar() + + ylab(y_label_text) + + xlab(type_name) + + scale_y_continuous(trans ="log10") + + theme_bw() + + if (!is.null(colour_col) & !is.null(colour_palette)) { + point_graph <- point_graph + + scale_colour_manual(values = colour_palette, + name = colour_col) + + scale_fill_manual(values = colour_palette, + name = colour_col) + + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5), + legend.position = "bottom") + } else if (!is.null(colour_col)) { + point_graph <- point_graph + + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5), + legend.position = "bottom") + } else { + point_graph <- point_graph + + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) + } + + if (use_sample_size) { + point_graph <- point_graph + + scale_shape_binned(name = "Number of\nisolates", + breaks = c(5,10,25,50,100)) + } + + return(point_graph) +} # Define serotype categories and palettes vaccine_types <- list( @@ -57,12 +169,15 @@ epi_colors <- c( The dataset used in this analysis is contained in the `S_pneumoniae_mixed_strain` object, which includes data from `r S_pneumoniae_mixed_strain %>% dplyr::select(study) %>% dplyr::n_distinct()` studies on `r S_pneumoniae_mixed_strain %>% dplyr::select(type) %>% dplyr::n_distinct()` serotypes. The distribution of samples between each study can be plotted, if they are ranked by the mean number of carriage and disease isolates: The total number of observations for each serotype can be plotted: -``` {r Plot distribution by serotype, include = FALSE} +``` {r Plot distribution by serotype} n_chains <- 2 n_iter <- 2.5e4 n_core <- 2 +adapt_delta = 0.99 +stepsize = 0.01 +max_treedepth = 20 serotype_by_count <- S_pneumoniae_mixed_strain %>% @@ -108,22 +223,26 @@ The study-adjusted type-specific model can be applied to the overall dataset: full_mixed_serotype_and_strain_invasiveness <- progressionEstimation::process_input_data(S_pneumoniae_mixed_strain, - combine_strain = TRUE, + use_strain = TRUE, condense = FALSE) -full_strain_and_serotype_specific_poisson_fit <- +full_adjusted_serotype_specific_strain_modified_poisson_fit <- progressionEstimation::fit_progression_rate_model(full_mixed_serotype_and_strain_invasiveness, type_specific = TRUE, location_adjustment = FALSE, + strain_as_secondary_type = TRUE, stat_model = "poisson", - model_description = "strain_and_serotype_specific_poisson", + model_description = "serotype_specific_strain_modified_poisson", num_chains = n_chains, num_iter = n_iter, - num_cores = n_core) + num_cores = n_core, + adapt_delta_value = adapt_delta, + stepsize_value = stepsize, + max_treedepth_value = max_treedepth) -rhat_plot <- plot(full_strain_and_serotype_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005) +rhat_plot <- plot(full_adjusted_serotype_specific_strain_modified_poisson_fit, plotfun = "rhat", binwidth = 0.00005) -trace_plot <- rstan::traceplot(full_strain_and_serotype_specific_poisson_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90)) +trace_plot <- rstan::traceplot(full_adjusted_serotype_specific_strain_modified_poisson_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90)) (full_strain_and_serotype_validation_plot <- cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot), @@ -144,9 +263,10 @@ ggsave(full_strain_and_serotype_validation_plot, # Annotate serotypes by status best_fitting_output <- - progressionEstimation::process_progression_rate_model_output(full_strain_and_serotype_specific_poisson_fit, + progressionEstimation::process_progression_rate_model_output(full_adjusted_serotype_specific_strain_modified_poisson_fit, S_pneumoniae_mixed_strain, - combined_strain_type = TRUE) %>% + strain_as_secondary_type = TRUE, + condense = FALSE) %>% dplyr::mutate("type" = S_pneumoniae_mixed_strain$type) %>% dplyr::mutate("classification" = dplyr::case_when( type %in% vaccine_types[["PCV7"]] ~ "PCV7", @@ -164,31 +284,70 @@ best_fitting_output <- "PCV15", "PCV20", "PPV23", - "No PCV"))) + "No PCV"))) %>% + tidyr::unite(combined,type,strain,remove = FALSE) %>% + dplyr::group_by(combined) %>% + dplyr::mutate(num_observations = sum(carriage+disease)) %>% + dplyr::ungroup() %>% + dplyr::filter(num_observations >= 10) %>% + dplyr::group_by(strain) %>% + dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>% + dplyr::ungroup() %>% + dplyr::group_by(type) %>% + dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>% + dplyr::ungroup() + +# Function needed if processing combined serotype/strain assignments +mixedrank = function(x) order(gtools::mixedorder(as.character(x))) # Order serotypes -strains_by_invasiveness <- +serotype_levels <- + best_fitting_output %>% + dplyr::select(type,classification) %>% + dplyr::distinct() %>% + dplyr::group_by(classification) %>% + dplyr::arrange(mixedrank(type), + .by_group = TRUE) %>% + dplyr::ungroup() %>% + dplyr::select(type) %>% + dplyr::mutate(type = as.character(type)) %>% + dplyr::pull() + +strain_levels <- gtools::mixedsort(best_fitting_output$strain) + +serotypes_by_invasiveness <- best_fitting_output %>% - dplyr::select(combined,nu) %>% + dplyr::select(type,nu) %>% dplyr::distinct() %>% dplyr::arrange(desc(nu)) %>% - dplyr::select(combined) %>% + dplyr::select(type) %>% + dplyr::mutate(type = as.character(type)) %>% + dplyr::pull() + +strains_by_invasiveness <- + best_fitting_output %>% + dplyr::select(strain,secondary_nu) %>% + dplyr::distinct() %>% + dplyr::arrange(desc(secondary_nu)) %>% + dplyr::select(strain) %>% + dplyr::mutate(strain = as.character(strain)) %>% dplyr::pull() best_fitting_output %<>% - dplyr::mutate(combined = factor(combined, levels = strains_by_invasiveness)) + dplyr::mutate(combined = factor(strain, levels = strains_by_invasiveness)) # Plot (full_invasiveness_plot <- - progressionEstimation::plot_progression_rates(best_fitting_output, - type = "combined", + plot_progression_rate_by_type(best_fitting_output %>% + dplyr::filter(num_strains > 1), + type = "strain", unit_time = "year", - type_name = "Serotype", + type_name = "Strain", colour_col = "classification", colour_palette = vaccine_colours, use_sample_size = TRUE) + - theme(axis.text.x = element_text(size = 6)) -) + facet_wrap(.~strain, + scales = 'free_x')) ggsave(full_invasiveness_plot, file = "full_mixed_strain_and_serotype_invasiveness_plot.png", @@ -203,90 +362,50 @@ ggsave(full_invasiveness_plot, ``` {r Plot only larger sample size} # Annotate sample size -best_fitting_output %<>% - dplyr::group_by(combined) %>% - dplyr::mutate(num_observations = sum(carriage+disease)) %>% - dplyr::ungroup() %>% - dplyr::filter(num_observations >= 10) %>% - dplyr::group_by(strain) %>% - dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>% - dplyr::ungroup() %>% - dplyr::group_by(type) %>% - dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>% - dplyr::ungroup() - -# Plot -(invasiveness_plot <- - progressionEstimation::plot_progression_rates(best_fitting_output, - type = "combined", - unit_time = "year", - type_name = "Serotype", - colour_col = "classification", - colour_palette = vaccine_colours, - use_sample_size = TRUE)) - -``` - -``` {r Plot variation within serotypes, fig.height = 12} - -mixedrank = function(x) order(gtools::mixedorder(as.character(x))) - -# Reorder by serotype -strain_and_serotype_levels <- - best_fitting_output %>% - dplyr::select(combined,classification) %>% - dplyr::distinct() %>% - dplyr::arrange(classification,combined) %>% - dplyr::select(combined) %>% - dplyr::pull() - -serotype_levels <- +filtered_best_fitting_output <- best_fitting_output %>% - dplyr::select(type,classification) %>% - dplyr::distinct() %>% - dplyr::group_by(classification) %>% - dplyr::arrange(mixedrank(type), - .by_group = TRUE) %>% + dplyr::group_by(combined) %>% + dplyr::mutate(num_observations = sum(carriage+disease)) %>% dplyr::ungroup() %>% - dplyr::select(type) %>% - dplyr::pull() - -best_fitting_output %<>% - dplyr::mutate(combined = factor(combined, levels = strain_and_serotype_levels)) %>% - dplyr::mutate(type = factor(type, levels = serotype_levels)) + dplyr::filter(num_observations >= 10) %>% + dplyr::group_by(strain) %>% + dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>% + dplyr::ungroup() %>% + dplyr::group_by(type) %>% + dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>% + dplyr::ungroup() -(serotype_invasiveness_plot <- - progressionEstimation::plot_progression_rates(best_fitting_output %>% +# Plot +(filtered_invasiveness_plot <- + plot_progression_rate_by_type(filtered_best_fitting_output %>% + dplyr::mutate(strain = factor(strain, levels = strains_by_invasiveness)) %>% + dplyr::mutate(type = factor(type, levels = serotype_levels)) %>% dplyr::filter(num_strains > 1), - type = "combined", + type = "strain", unit_time = "year", - type_name = "Serotype", + type_name = "Strain", colour_col = "classification", colour_palette = vaccine_colours, use_sample_size = TRUE) + facet_wrap(.~type, - ncol = 2, scales = 'free_x')) -``` - - -``` {r Plot variation within strains, fig.height = 12} - -strain_levels <- - best_fitting_output %>% - dplyr::select(strain) %>% - dplyr::distinct() %>% - dplyr::arrange(mixedrank(strain)) %>% - dplyr::pull() +ggsave(filtered_invasiveness_plot, + file = "filtered_mixed_strain_and_serotype_invasiveness_plot.png", + width = 20, + height = 10 +) -best_fitting_output %<>% - dplyr::mutate(strain = factor(strain, levels = strain_levels)) +``` +``` {r Joint plot for mixed strain invasiveness} -(strain_invasiveness_plot <- - progressionEstimation::plot_progression_rates(best_fitting_output %>% - dplyr::filter(num_serotypes > 1), - type = "combined", +# Plot +(filtered_sero_invasiveness_plot <- + plot_progression_rate_by_type(filtered_best_fitting_output %>% + dplyr::filter(num_serotypes > 1) %>% + dplyr::mutate(strain = factor(strain, levels = strains_by_invasiveness)) %>% + dplyr::mutate(type = factor(type, levels = serotypes_by_invasiveness)), + type = "type", unit_time = "year", type_name = "Serotype", colour_col = "classification", @@ -295,16 +414,18 @@ best_fitting_output %<>% facet_wrap(.~strain, scales = 'free_x')) -combined_heterogeneity_plot <- - cowplot::plot_grid(plotlist = list(strain_invasiveness_plot, serotype_invasiveness_plot), - ncol = 1, nrow = 2, - rel_heights = c(0.5, 1), - labels = "AUTO") - -ggsave(combined_heterogeneity_plot, - file = "mixed_within_strain_invasiveness_variation_plot.png", - width = 12, - height = 17.5 -) - +(combined_mixed_strain_invasiveness_plot <- + cowplot::plot_grid(plotlist = list(filtered_sero_invasiveness_plot + + ylab("Progression rate contribution\n(disease per carrier per year)") + + theme(legend.position = "none"), + filtered_invasiveness_plot + + ylab("Progression rate contribution\n(disease per carrier per year)")), + labels = "AUTO", + nrow = 2, + rel_heights = c(0.3,0.7))) + +ggsave(combined_mixed_strain_invasiveness_plot, + file = "combined_mixed_strain_invasiveness_plot.png", + height = 12, + width = 9) ``` diff --git a/examples/s-pneumoniae-strain-invasiveness-adults.html b/examples/s-pneumoniae-strain-invasiveness-adults.html index a1ec602..6c9abd8 100644 --- a/examples/s-pneumoniae-strain-invasiveness-adults.html +++ b/examples/s-pneumoniae-strain-invasiveness-adults.html @@ -14,6 +14,7 @@ S. pneumoniae strain invasiveness in adults + + @@ -318,199 +141,255 @@

S. pneumoniae strain invasiveness in adult -
#> Writing NAMESPACE
-#> Writing NAMESPACE

Description and filtering of the dataset

The dataset used in this analysis is contained in the S_pneumoniae_mixed_strain object, which includes data from 1 studies on 11 serotypes. The distribution of samples between each study can be plotted, if they are ranked by the mean number of carriage and disease isolates: The total number of observations for each serotype can be plotted:

+

+
+n_chains <- 2
+n_iter <- 2.5e4
+n_core <- 2
+adapt_delta = 0.99
+stepsize = 0.01
+max_treedepth = 20
+
+serotype_by_count <-
+  S_pneumoniae_mixed_strain %>%
+    group_by(type) %>%
+    dplyr::mutate(total_count = sum(carriage)+sum(disease)) %>%
+    dplyr::select(type,total_count) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(total_count)) %>%
+    dplyr::select(type) %>%
+    dplyr::pull()
+
+S_pneumoniae_mixed_strain %<>%
+  dplyr::mutate(type = factor(type, levels = serotype_by_count)) %>%
+  dplyr::mutate(study = factor(study))
+
+mixed_strain_serotype_distribution_plot <-
+  ggplot(S_pneumoniae_mixed_strain %>%
+           tidyr::pivot_longer(c(carriage,disease),
+                               names_to = "Sample type",
+                               values_to = "count"),
+         aes(x = type,
+             y = count,
+             colour = `Sample type`,
+             fill = `Sample type`)) +
+    geom_col() +
+    xlab("Serotype") +
+    theme_bw() + 
+    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
+    scale_fill_manual(values = epi_colors) +
+    scale_colour_manual(values = epi_colors)
+
+ggsave(mixed_strain_serotype_distribution_plot,
+       file = "mixed_strain_serotype_distribution_plot.png",
+       height = 6,
+       width = 6
+)

The study-adjusted type-specific model can be applied to the overall dataset:

- -

- - -

- - -

- -

- -

- +

+full_mixed_serotype_and_strain_invasiveness <- 
+  progressionEstimation::process_input_data(S_pneumoniae_mixed_strain,
+                                            use_strain = TRUE,
+                                            condense = FALSE)
+
+full_adjusted_serotype_specific_strain_modified_poisson_fit <- 
+  progressionEstimation::fit_progression_rate_model(full_mixed_serotype_and_strain_invasiveness,
+                                                    type_specific = TRUE,
+                                                    location_adjustment = FALSE,
+                                                    strain_as_secondary_type = TRUE,
+                                                    stat_model = "poisson",
+                                                    model_description = "serotype_specific_strain_modified_poisson",
+                                                    num_chains = n_chains,
+                                                    num_iter = n_iter,
+                                                    num_cores = n_core,
+                                                    adapt_delta_value = adapt_delta,
+                                                    stepsize_value = stepsize,
+                                                    max_treedepth_value = max_treedepth)
+
+rhat_plot <- plot(full_adjusted_serotype_specific_strain_modified_poisson_fit, plotfun = "rhat", binwidth = 0.00005)
+
+trace_plot <- rstan::traceplot(full_adjusted_serotype_specific_strain_modified_poisson_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90))
+
+(full_strain_and_serotype_validation_plot <-
+  cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
+                     nrow = 1,
+                     ncol = 2,
+                     labels = "AUTO")
+)
+#> Warning: Removed 2 rows containing non-finite values (stat_bin).
+

+

+ggsave(full_strain_and_serotype_validation_plot,
+       file = "full_mixed_strain_and_serotype_validation_plot.png",
+       width = 7,
+       height = 5
+)
+

+# Annotate serotypes by status
+best_fitting_output <- 
+  progressionEstimation::process_progression_rate_model_output(full_adjusted_serotype_specific_strain_modified_poisson_fit,
+                                                               S_pneumoniae_mixed_strain,
+                                                               strain_as_secondary_type = TRUE,
+                                                               condense = FALSE) %>%
+    dplyr::mutate("type" = S_pneumoniae_mixed_strain$type) %>%
+    dplyr::mutate("classification" = dplyr::case_when(
+        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
+        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
+        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
+        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
+        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
+        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
+        TRUE ~ "No PCV"
+      )
+    ) %>%
+    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                     "PCV10",
+                                                                     "PCV13",
+                                                                     "PCV15",
+                                                                     "PCV20",
+                                                                     "PPV23",
+                                                                     "No PCV"))) %>%
+    tidyr::unite(combined,type,strain,remove = FALSE) %>%
+    dplyr::group_by(combined) %>%
+    dplyr::mutate(num_observations = sum(carriage+disease)) %>%
+    dplyr::ungroup() %>%
+    dplyr::filter(num_observations >= 10) %>%
+    dplyr::group_by(strain) %>%
+    dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>%
+    dplyr::ungroup() %>%
+    dplyr::group_by(type) %>%
+    dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>%
+    dplyr::ungroup()
+
+# Function needed if processing combined serotype/strain assignments
+mixedrank = function(x) order(gtools::mixedorder(as.character(x)))
+
+# Order serotypes
+serotype_levels <-
+  best_fitting_output %>%
+    dplyr::select(type,classification) %>%
+    dplyr::distinct() %>%
+    dplyr::group_by(classification) %>%
+    dplyr::arrange(mixedrank(type),
+                   .by_group = TRUE) %>%
+    dplyr::ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::mutate(type = as.character(type)) %>%
+    dplyr::pull()
+
+strain_levels <- gtools::mixedsort(best_fitting_output$strain)
+
+serotypes_by_invasiveness <-
+  best_fitting_output %>%
+    dplyr::select(type,nu) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(nu)) %>%
+    dplyr::select(type) %>%
+    dplyr::mutate(type = as.character(type)) %>%
+    dplyr::pull()
+
+strains_by_invasiveness <-
+  best_fitting_output %>%
+    dplyr::select(strain,secondary_nu) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(secondary_nu)) %>%
+    dplyr::select(strain) %>%
+    dplyr::mutate(strain = as.character(strain)) %>%
+    dplyr::pull()
+
+best_fitting_output %<>%
+  dplyr::mutate(combined = factor(strain, levels = strains_by_invasiveness))
+
+# Plot
+(full_invasiveness_plot <-
+  plot_progression_rate_by_type(best_fitting_output %>%
+                                                  dplyr::filter(num_strains > 1),
+                                                type = "strain",
+                                                unit_time = "year",
+                                                type_name = "Strain",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE) +
+                                                facet_wrap(.~strain,
+                                                           scales = 'free_x'))
+

+

+ggsave(full_invasiveness_plot,
+       file = "full_mixed_strain_and_serotype_invasiveness_plot.png",
+       width = 20,
+       height = 10
+)
+

+# Annotate sample size
+filtered_best_fitting_output <-
+  best_fitting_output %>%
+    dplyr::group_by(combined) %>%
+    dplyr::mutate(num_observations = sum(carriage+disease)) %>%
+    dplyr::ungroup() %>%
+    dplyr::filter(num_observations >= 10) %>%
+    dplyr::group_by(strain) %>%
+    dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>%
+    dplyr::ungroup() %>%
+    dplyr::group_by(type) %>%
+    dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>%
+    dplyr::ungroup()
+
+# Plot
+(filtered_invasiveness_plot <-
+  plot_progression_rate_by_type(filtered_best_fitting_output %>%
+                                  dplyr::mutate(strain = factor(strain, levels = strains_by_invasiveness)) %>%
+                                  dplyr::mutate(type = factor(type, levels = serotype_levels)) %>%
+                                                  dplyr::filter(num_strains > 1),
+                                                type = "strain",
+                                                unit_time = "year",
+                                                type_name = "Strain",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE) +
+                                                facet_wrap(.~type,
+                                                           scales = 'free_x'))
+

+

+ggsave(filtered_invasiveness_plot,
+       file = "filtered_mixed_strain_and_serotype_invasiveness_plot.png",
+       width = 20,
+       height = 10
+)
+

+# Plot
+(filtered_sero_invasiveness_plot <-
+  plot_progression_rate_by_type(filtered_best_fitting_output %>%
+                                    dplyr::filter(num_serotypes > 1) %>%
+                                    dplyr::mutate(strain = factor(strain, levels = strains_by_invasiveness)) %>%
+                                    dplyr::mutate(type = factor(type, levels = serotypes_by_invasiveness)),
+                                                type = "type",
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE) +
+                                                facet_wrap(.~strain,
+                                                           scales = 'free_x'))
+

+

+(combined_mixed_strain_invasiveness_plot <-
+  cowplot::plot_grid(plotlist = list(filtered_sero_invasiveness_plot +
+                                       ylab("Progression rate contribution\n(disease per carrier per year)") +
+                                       theme(legend.position = "none"),
+                                     filtered_invasiveness_plot +
+                                       ylab("Progression rate contribution\n(disease per carrier per year)")),
+                     labels = "AUTO",
+                     nrow = 2,
+                     rel_heights = c(0.3,0.7)))
+

+

+ggsave(combined_mixed_strain_invasiveness_plot,
+       file = "combined_mixed_strain_invasiveness_plot.png",
+       height = 12,
+       width = 9)
diff --git a/examples/s-pneumoniae-strain-invasiveness.Rmd b/examples/s-pneumoniae-strain-invasiveness.Rmd index 1b0ac81..e654fb6 100644 --- a/examples/s-pneumoniae-strain-invasiveness.Rmd +++ b/examples/s-pneumoniae-strain-invasiveness.Rmd @@ -11,7 +11,7 @@ knitr::opts_chunk$set( ) ``` -```{r setup} +```{r setup, include = FALSE} # Load dependencies require(tidyverse) require(magrittr) @@ -24,8 +24,124 @@ require(xlsx) require(gtools) # Load stan package library(progressionEstimation) -pkgbuild::compile_dll() -roxygen2::roxygenize(package.dir = "..") +#pkgbuild::compile_dll() +#roxygen2::roxygenize(package.dir = "..") + +############# +# Functions # +############# + +plot_progression_rate_by_type <- function(model_output_df, + type = "type", + unit_time = "unit time", + type_name = "type", + colour_col = NULL, + colour_palette = NULL, + use_sample_size = FALSE) { + if (!(any(grepl("nu",colnames(model_output_df))))) { + stop("Need to include model output in data frame for plotting") + } + progression_rate_values <- c("nu", "nu_lower", "nu_upper") + if (type == "strain") { + progression_rate_values <- paste0("secondary_", progression_rate_values) + } + y_label_text = paste0("Progression rate contribution (disease per carrier per ",unit_time,")") + + model_output_df %<>% + dplyr::group_by(!!! dplyr::syms(type)) %>% + dplyr::mutate(num_observations = sum(carriage+disease)) %>% + dplyr::ungroup() + + if (type == "type") { + model_output_df %<>% + dplyr::group_by(!!! dplyr::syms(type),strain) %>% + dplyr::slice_head(n=1) %>% + dplyr::ungroup() + } else if (type == "strain") { + model_output_df %<>% + dplyr::group_by(!!! dplyr::syms(type),type) %>% + dplyr::slice_head(n=1) %>% + dplyr::ungroup() + } + + if (is.null(colour_col)) { + if (use_sample_size) { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]), + shape = num_observations)) + } else { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]))) + } + } else { + if (use_sample_size) { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]), + colour = get(colour_col), + fill = get(colour_col), + shape = num_observations)) + } else { + base_graph <- + ggplot(model_output_df, + aes(x = get(!!type), + y = get(progression_rate_values[1]), + ymin = get(progression_rate_values[2]), + ymax = get(progression_rate_values[3]), + colour = get(colour_col), + fill = get(colour_col))) + } + } + + point_graph <- + base_graph + + geom_point() + + geom_errorbar() + + ylab(y_label_text) + + xlab(type_name) + + scale_y_continuous(trans ="log10") + + theme_bw() + + if (!is.null(colour_col) & !is.null(colour_palette)) { + point_graph <- point_graph + + scale_colour_manual(values = colour_palette, + name = colour_col) + + scale_fill_manual(values = colour_palette, + name = colour_col) + + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5), + legend.position = "bottom") + } else if (!is.null(colour_col)) { + point_graph <- point_graph + + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5), + legend.position = "bottom") + } else { + point_graph <- point_graph + + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) + } + + if (use_sample_size) { + point_graph <- point_graph + + scale_shape_binned(name = "Number of\nisolates", + breaks = c(5,10,25,50,100)) + } + + return(point_graph) +} + +################### +# Data structures # +################### # Define serotype categories and palettes vaccine_types <- list( @@ -160,7 +276,7 @@ ggsave(combined_full_epi_data_plot, ``` -As many of these serotypes are rare, to facilitate model fitting, we exclude any serotype for which the maximum number of observations is below five: +As many of these serotypes are rare, to facilitate model fitting, we exclude any serotype for which the maximum number of observations is below five, and any serotype found in fewer than five strains, and any strain associated with fewer than five serotypes: ``` {r Plot distribution by serotype in filtered dataset, include = FALSE} @@ -168,7 +284,14 @@ threshold_count <- 5 filtered_S_pneumoniae_infant_strain <- S_pneumoniae_infant_strain %>% - dplyr::filter(carriage >= threshold_count | disease >= threshold_count) + dplyr::filter(carriage >= threshold_count | disease >= threshold_count) %>% + dplyr::group_by(type) %>% + dplyr::mutate(strain_count = n_distinct(strain)) %>% + dplyr::ungroup() %>% + dplyr::group_by(strain) %>% + dplyr::mutate(type_count = n_distinct(type)) %>% + dplyr::ungroup() %>% + dplyr::filter(strain_count >= threshold_count | type_count >= threshold_count) filtered_S_pneumoniae_infant_strain %<>% dplyr::mutate(study = factor(study, levels = studies_by_size[studies_by_size %in% unique(filtered_S_pneumoniae_infant_strain$study)])) @@ -249,7 +372,7 @@ ggsave(combined_filtered_epi_data_plot, ``` -This filtered dataset comprises `r filtered_S_pneumoniae_infant_strain %>% dplyr::select(type) %>% dplyr::n_distinct()` serotypes. +This filtered dataset comprises `r nrow(filtered_S_pneumoniae_infant_strain)` isolates of `r filtered_S_pneumoniae_infant_strain %>% dplyr::select(type) %>% dplyr::n_distinct()` serotypes, `r filtered_S_pneumoniae_infant_strain %>% dplyr::select(strain) %>% dplyr::n_distinct()` strains, and `r filtered_S_pneumoniae_infant_strain %>% tidyr::unite(combined,strain,type) %>% dplyr::select(combined) %>% dplyr::n_distinct()` strain-serotype combinations. ## Fitting the statistical models @@ -366,7 +489,7 @@ adjusted_strain_specific_negbin_output_df <- ``` -Models can also combine serotype and strain information, with invasiveness primarily determined by serotype, and modified by strain: +Models can also combine serotype and strain information, with **invasiveness primarily determined by serotype, and modified by strain**: $$d_{i,j,k} \sim Poisson(\delta_{i}\nu_{k}\nu_{k}\rho_{i,j,k}N_{i}t_{i})$$ @@ -422,7 +545,7 @@ adjusted_serotype_specific_strain_modified_negbin_output_df <- ``` -Models can alternative have invasiveness primarily determined by strain, and modified by serotype: +Models can alternative have **invasiveness primarily determined by strain, and modified by serotype**: $$d_{i,j,k} \sim Poisson(\delta_{i}\nu_{k}\nu_{k}\rho_{i,j,k}N_{i}t_{i})$$ @@ -478,7 +601,7 @@ adjusted_strain_specific_serotype_modified_negbin_output_df <- ``` -The final model structure assigns a different invasiveness to each strain-serotype combination: +The final model structure assigns a **different invasiveness to each strain-serotype combination**: $$d_{i,j,k} \sim Poisson(\delta_{i}\nu_{j,k}\rho_{i,j,k}N_{i}t_{i})$$ @@ -640,11 +763,11 @@ no_leg_plot <- cowplot::plot_grid(plotlist = prediction_plots, prediction_plot_legend <- progressionEstimation::plot_case_carrier_predictions(model_outputs[[1]], just_legend = TRUE) -pred_v_obs_plot <- +(pred_v_obs_plot <- cowplot::plot_grid(no_leg_plot, prediction_plot_legend, ncol = 1, - rel_heights = c(1,0.1)) + rel_heights = c(1,0.1))) ggsave(pred_v_obs_plot, file = "infant_strain_serotypes_pred_v_obs_plot.png", @@ -655,7 +778,7 @@ ggsave(pred_v_obs_plot, The deviation of the predicted and observed values can be simply evaluated using the root mean square error: -``` {r Calculate RMSE} +``` {r Calculate RMSE, fig.height = 10} obs_pred_df <- dplyr::bind_rows(model_outputs) %>% @@ -708,7 +831,7 @@ ggsave(strain_and_serotype_rmse_plot, The fits of the negative binomial can be evaluated through plotting the estimates of the precision parameter, $\phi$. As $\phi$ increases, the variance of the negative binomial distribution decreases, and the negative binomal model becomes more similar to the Poisson model. -``` {r Plot precision parameters for negative binomial models, fig.width = 6} +``` {r Plot precision parameters for negative binomial models, fig.width = 6, fig.height = 10} (strain_and_serotype_precision_parameters <- ggplot(obs_pred_df %>% @@ -744,7 +867,25 @@ To check these are not being constrained by the prior limits, we plot the invasi ``` {r Secondary invasiveness in the type-specific strain-modified Poisson model} -progressionEstimation::plot_progression_rates(model_outputs[[5]], type = "strain") +order_strains <- + model_outputs[[5]] %>% + dplyr::select(strain,secondary_nu) %>% + dplyr::distinct() %>% + dplyr::arrange(desc(secondary_nu)) %>% + dplyr::select(strain) %>% + dplyr::mutate(strain = as.character(strain)) %>% + dplyr::pull() + +(strain_inv <- + progressionEstimation::plot_progression_rates(model_outputs[[5]] %>% + dplyr::mutate(strain = factor(strain, + levels = order_strains)), + type = "strain")) + +ggsave(strain_inv, + file = "type_specific_strain_modified_strain_invasiveness.png", + width = 8, + height = 6) ``` @@ -770,7 +911,7 @@ progressionEstimation::plot_progression_rates(model_outputs[[8]]) The model likelihoods can be compared using leave-one-out cross-validation: -``` {r Comparison with LOO-CV using full log likelihood, include = FALSE} +``` {r Comparison with LOO-CV using full log likelihood} loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list, use_moments = FALSE, @@ -780,11 +921,16 @@ loo_comparison %>% kableExtra::kable() %>% kableExtra::kable_styling(latex_options = "scale_down") +write.csv(loo_comparison, + file = "child_strain_loo_comparison.csv", + quote = FALSE, + row.names = TRUE) + ``` -The Pareto distribution k values are too high for robust estimates of the ELPD. This reflects many of the points being +The Pareto distribution k values are too high for robust estimates of the ELPD. This reflects there being too few observations per parameter for this type of evaluation. Even usingt the disease likelihoods, we cannot calculate an accuraste cross-validation: -``` {r Comparison with LOO-CV using disease distribution log likelihood, include = FALSE} +``` {r Comparison with LOO-CV using disease distribution log likelihood} disease_loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list, log_lik_param = "disease_log_lik", @@ -795,13 +941,18 @@ disease_loo_comparison %>% kableExtra::kable() %>% kableExtra::kable_styling(latex_options = "scale_down") +write.csv(disease_loo_comparison, + file = "child_strain_disease_loo_comparison.csv", + quote = FALSE, + row.names = TRUE) + ``` ## Run model comparison with Bayes factors As the models can instead be compared with Bayes factors: -``` {r Comparison with BF, include = FALSE} +``` {r Comparison with BF} bf_comparison <- progressionEstimation::compare_model_fits_with_bf(fit_list, num_iter = n_iter, @@ -810,6 +961,11 @@ bf_comparison %>% kableExtra::kable() %>% kableExtra::kable_styling(latex_options = "scale_down") +write.csv(bf_comparison, + file = "child_strain_bf_comparison.csv", + quote = FALSE, + row.names = FALSE) + ``` ## Plot serotype invasiveness @@ -818,17 +974,19 @@ The best-fitting model can then be applied to the overall dataset. ``` {r Plot invasiveness estimates from best-fitting model} +# Generate input for strain and serotype models full_infant_serotype_and_strain_invasiveness <- progressionEstimation::process_input_data(S_pneumoniae_infant_strain, - combine_strain = TRUE, + use_strain = TRUE, condense = FALSE) -full_adjusted_strain_and_serotype_specific_poisson_fit <- +full_adjusted_serotype_specific_strain_modified_poisson_fit <- progressionEstimation::fit_progression_rate_model(full_infant_serotype_and_strain_invasiveness, type_specific = TRUE, location_adjustment = TRUE, + strain_as_secondary_type = TRUE, stat_model = "poisson", - model_description = "strain_and_serotype_specific_poisson", + model_description = "serotype_specific_strain_modified_poisson", num_chains = n_chains, num_iter = n_iter, num_cores = n_core, @@ -836,9 +994,13 @@ full_adjusted_strain_and_serotype_specific_poisson_fit <- stepsize_value = stepsize, max_treedepth_value = max_treedepth) -rhat_plot <- plot(full_adjusted_strain_and_serotype_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005) +rhat_plot <- plot(full_adjusted_serotype_specific_strain_modified_poisson_fit, + plotfun = "rhat", + binwidth = 0.00005) -trace_plot <- rstan::traceplot(full_adjusted_strain_and_serotype_specific_poisson_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90)) +trace_plot <- rstan::traceplot(full_adjusted_serotype_specific_strain_modified_poisson_fit, + pars = "lp__") + + theme(axis.text.x = element_text(angle = 90)) (full_strain_and_serotype_validation_plot <- cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot), @@ -859,9 +1021,10 @@ ggsave(full_strain_and_serotype_validation_plot, # Annotate serotypes by status best_fitting_output <- - progressionEstimation::process_progression_rate_model_output(full_adjusted_strain_and_serotype_specific_poisson_fit, + progressionEstimation::process_progression_rate_model_output(full_adjusted_serotype_specific_strain_modified_poisson_fit, S_pneumoniae_infant_strain, - combined_strain_type = TRUE) %>% + strain_as_secondary_type = TRUE, + condense = FALSE) %>% dplyr::mutate("type" = S_pneumoniae_infant_strain$type) %>% dplyr::mutate("classification" = dplyr::case_when( type %in% vaccine_types[["PCV7"]] ~ "PCV7", @@ -879,33 +1042,66 @@ best_fitting_output <- "PCV15", "PCV20", "PPV23", - "No PCV"))) + "No PCV"))) %>% + dplyr::mutate(combined_nu = nu * secondary_nu) %>% + tidyr::unite(combined, + type,strain, + sep = "_", + remove = FALSE) # Order serotypes -strains_by_invasiveness <- +serotypes_by_invasiveness <- best_fitting_output %>% - dplyr::select(combined,nu) %>% + dplyr::select(type,nu) %>% dplyr::distinct() %>% dplyr::arrange(desc(nu)) %>% - dplyr::select(combined) %>% + dplyr::select(type) %>% + dplyr::mutate(type = as.character(type)) %>% + dplyr::pull() + +# Order strains +strains_by_invasiveness <- + best_fitting_output %>% + dplyr::select(strain,secondary_nu) %>% + dplyr::distinct() %>% + dplyr::arrange(desc(secondary_nu)) %>% + dplyr::select(strain) %>% + dplyr::mutate(strain = as.character(strain)) %>% dplyr::pull() best_fitting_output %<>% - dplyr::mutate(combined = factor(combined, levels = strains_by_invasiveness)) + dplyr::mutate(type = factor(type, levels = serotypes_by_invasiveness)) %>% + dplyr::mutate(strain = factor(strain, levels = strains_by_invasiveness)) # Plot -(full_invasiveness_plot <- +strain_invasiveness <- progressionEstimation::plot_progression_rates(best_fitting_output, - type = "combined", + type = "strain", + unit_time = "year", + type_name = "GPSC", + use_sample_size = TRUE) + + ylab("Progression rate contribution\n(disease per carrier per year)") + + theme(axis.text.x = element_text(size = 6)) + +type_invasiveness <- + progressionEstimation::plot_progression_rates(best_fitting_output, + type = "type", unit_time = "year", type_name = "Serotype", colour_col = "classification", colour_palette = vaccine_colours, use_sample_size = TRUE) + + ylab("Progression rate contribution\n(disease per carrier per year)") + theme(axis.text.x = element_text(size = 6)) -) -ggsave(full_invasiveness_plot, +(joint_invasiveness <- + cowplot::plot_grid(plotlist = list(strain_invasiveness + theme(legend.position = "none"), + type_invasiveness), + labels = "AUTO", + nrow = 2, + rel_heights = c(1,1.25))) + +ggsave(joint_invasiveness, file = "full_strain_and_serotype_invasiveness_plot.png", width = 20, height = 10 @@ -913,17 +1109,78 @@ ggsave(full_invasiveness_plot, ``` + +``` {r Alternative plot of combined nu} + +not_in_current_vaccines <- c("No PCV","PPV23","PCV20","PCV15") + +combined_levels <- + best_fitting_output %>% + dplyr::select(combined,combined_nu) %>% + dplyr::distinct() %>% + dplyr::arrange(desc(combined_nu)) %>% + dplyr::select(combined) %>% + dplyr::mutate(combined = as.character(combined)) %>% + dplyr::pull() + +best_fitting_output %<>% + dplyr::mutate(combined = factor(combined, levels = combined_levels)) + +(all_combined_invasiveness <- + ggplot(best_fitting_output %>% + dplyr::select(combined,combined_nu, classification), + aes(x = combined, + y = combined_nu, + colour = classification, + label = combined)) + + geom_point() + + scale_y_continuous(trans = "log10") + + ylab(expression(nu~"(disease per carrier per year)")) + + scale_colour_manual(values = vaccine_colours) + + xlab("Combined serotype-strain genotype") + + theme_bw() + + theme(axis.text.x = element_text(angle = 90, + hjust = 1, + vjust = 0.5, + size = 3.5), + legend.position = "bottom") + + ggrepel::geom_label_repel(data = best_fitting_output %>% + dplyr::select(combined,combined_nu, classification) %>% + dplyr::filter(classification %in% not_in_current_vaccines[1:2]) %>% + dplyr::filter(combined_nu > 10**(-4)) %>% + dplyr::distinct(), + aes(label = combined), + force_pull = 0.0, + force = 10, + direction = "y", + size = 4, + max.overlaps = 20) +) + +ggsave(all_combined_invasiveness, + file = "combined_invasiveness_for_all_genotypes.png", + width = 11, + height = 8) + +``` + ## Save overall dataset ``` {r Save dataset} write.csv(best_fitting_output %>% - dplyr::select(combined,nu,nu_lower,nu_upper) %>% + dplyr::select(combined,type,strain, + nu,nu_lower,nu_upper, + secondary_nu,secondary_nu_lower,secondary_nu_upper) %>% dplyr::rename(genotype = combined) %>% - dplyr::rename(invasiveness = nu) %>% - dplyr::rename(invasiveness_lower = nu_lower) %>% - dplyr::rename(invasiveness_upper = nu_upper) %>% - dplyr::distinct(), + dplyr::rename(serotype_invasiveness = nu) %>% + dplyr::rename(serotype_invasiveness_lower = nu_lower) %>% + dplyr::rename(serotype_invasiveness_upper = nu_upper) %>% + dplyr::rename(strain_invasiveness = secondary_nu) %>% + dplyr::rename(strain_invasiveness_lower = secondary_nu_lower) %>% + dplyr::rename(strain_invasiveness_upper = secondary_nu_upper) %>% + dplyr::distinct() %>% + dplyr::arrange(genotype), file = "Dataset_S3.csv", quote = F, row.names = F) @@ -935,45 +1192,61 @@ write.csv(best_fitting_output %>% ``` {r Plot only larger sample size} # Annotate sample size -best_fitting_output %<>% - dplyr::group_by(combined) %>% - dplyr::mutate(num_observations = sum(carriage+disease)) %>% - dplyr::ungroup() %>% - dplyr::filter(num_observations >= 10) %>% - dplyr::group_by(strain) %>% - dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>% - dplyr::ungroup() %>% - dplyr::group_by(type) %>% - dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>% - dplyr::ungroup() +filtered_best_fitting_output <- + best_fitting_output %>% + dplyr::group_by(combined) %>% + dplyr::mutate(num_observations = sum(carriage+disease)) %>% + dplyr::ungroup() %>% + dplyr::filter(num_observations >= 10) %>% + dplyr::group_by(strain) %>% + dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>% + dplyr::ungroup() %>% + dplyr::group_by(type) %>% + dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>% + dplyr::ungroup() # Plot -(invasiveness_plot <- - progressionEstimation::plot_progression_rates(best_fitting_output, - type = "combined", +filtered_strain_invasiveness <- + progressionEstimation::plot_progression_rates(filtered_best_fitting_output, + type = "strain", + unit_time = "year", + type_name = "GPSC", + use_sample_size = TRUE) + + theme(axis.text.x = element_text(size = 6)) + +filtered_type_invasiveness <- + progressionEstimation::plot_progression_rates(filtered_best_fitting_output, + type = "type", unit_time = "year", type_name = "Serotype", colour_col = "classification", colour_palette = vaccine_colours, - use_sample_size = TRUE)) + use_sample_size = TRUE) + + theme(axis.text.x = element_text(size = 6)) + +(filtered_joint_invasiveness <- + cowplot::plot_grid(plotlist = list(filtered_strain_invasiveness + theme(legend.position = "none"), + filtered_type_invasiveness), + labels = "AUTO", + nrow = 2, + rel_heights = c(1,1.25))) + +ggsave(filtered_joint_invasiveness, + file = "filtered_full_strain_and_serotype_invasiveness_plot.png", + width = 20, + height = 10 +) ``` ``` {r Plot variation within serotypes, fig.height = 12} +# Function needed if processing combined serotype/strain assignments mixedrank = function(x) order(gtools::mixedorder(as.character(x))) # Reorder by serotype -strain_and_serotype_levels <- - best_fitting_output %>% - dplyr::select(combined,classification) %>% - dplyr::distinct() %>% - dplyr::arrange(classification,combined) %>% - dplyr::select(combined) %>% - dplyr::pull() - serotype_levels <- - best_fitting_output %>% + filtered_best_fitting_output %>% dplyr::select(type,classification) %>% dplyr::distinct() %>% dplyr::group_by(classification) %>% @@ -981,18 +1254,29 @@ serotype_levels <- .by_group = TRUE) %>% dplyr::ungroup() %>% dplyr::select(type) %>% + dplyr::mutate(as.character(type)) %>% dplyr::pull() -best_fitting_output %<>% - dplyr::mutate(combined = factor(combined, levels = strain_and_serotype_levels)) %>% +# Reorder by strain +strain_levels <- + filtered_best_fitting_output %>% + dplyr::select(strain,secondary_nu) %>% + dplyr::distinct() %>% + dplyr::arrange(desc(secondary_nu)) %>% + dplyr::select(strain) %>% + dplyr::mutate(as.character(strain)) %>% + dplyr::pull() + +filtered_best_fitting_output %<>% + dplyr::mutate(strain = factor(strain, levels = strain_levels)) %>% dplyr::mutate(type = factor(type, levels = serotype_levels)) (serotype_invasiveness_plot <- - progressionEstimation::plot_progression_rates(best_fitting_output %>% + plot_progression_rate_by_type(filtered_best_fitting_output %>% dplyr::filter(num_strains > 1), - type = "combined", + type = "strain", unit_time = "year", - type_name = "Serotype", + type_name = "Strain", colour_col = "classification", colour_palette = vaccine_colours, use_sample_size = TRUE) + @@ -1005,32 +1289,54 @@ ggsave(serotype_invasiveness_plot, height = 12 ) +ggsave(serotype_invasiveness_plot, + file = "within_serotype_invasiveness_variation_plot.pdf", + width = 8, + height = 12 +) + ``` ``` {r Plot variation within strains, fig.height = 12} -strain_levels <- - best_fitting_output %>% - dplyr::select(strain) %>% +# Reorder by serotype +serotype_levels <- + filtered_best_fitting_output %>% + dplyr::select(type,nu) %>% dplyr::distinct() %>% - dplyr::arrange(mixedrank(strain)) %>% + dplyr::arrange(desc(nu)) %>% + dplyr::ungroup() %>% + dplyr::select(type) %>% + dplyr::mutate(as.character(type)) %>% dplyr::pull() -best_fitting_output %<>% - dplyr::mutate(strain = factor(strain, levels = strain_levels)) +# Reorder by strain +strain_levels <- + gtools::mixedsort( + filtered_best_fitting_output %>% + dplyr::select(strain) %>% + dplyr::distinct() %>% + dplyr::mutate(strain = as.character(strain)) %>% + dplyr::pull() + ) + +filtered_best_fitting_output %<>% + dplyr::mutate(strain = factor(strain, levels = strain_levels)) %>% + dplyr::mutate(type = factor(type, levels = serotype_levels)) (strain_invasiveness_plot <- - progressionEstimation::plot_progression_rates(best_fitting_output %>% - dplyr::filter(num_serotypes > 1), - type = "combined", - unit_time = "year", - type_name = "Serotype", - colour_col = "classification", - colour_palette = vaccine_colours, - use_sample_size = TRUE) + - facet_wrap(.~strain, - scales = 'free_x')) + plot_progression_rate_by_type(filtered_best_fitting_output %>% + dplyr::filter(num_serotypes > 1), + type = "type", + unit_time = "year", + type_name = "Serotype", + colour_col = "classification", + colour_palette = vaccine_colours, + use_sample_size = TRUE) + + facet_wrap(.~strain, + scales = 'free_x') +) ggsave(strain_invasiveness_plot, file = "within_strain_invasiveness_variation_plot.png", @@ -1038,6 +1344,12 @@ ggsave(strain_invasiveness_plot, height = 8 ) +ggsave(strain_invasiveness_plot, + file = "within_strain_invasiveness_variation_plot.pdf", + width = 8, + height = 8 +) + ``` ## Plot study-specific scale factors @@ -1064,7 +1376,14 @@ sensitivity_S_pneumoniae_infant_strain <- study %in% c("Finland.Pre.PCV","Oxford.pre.PCV","Stockholm.pre.PCV") ~ as.integer(carriage_samples*100), TRUE ~ carriage_samples ) - ) + ) %>% + dplyr::group_by(type) %>% + dplyr::mutate(strain_count = n_distinct(strain)) %>% + dplyr::ungroup() %>% + dplyr::group_by(strain) %>% + dplyr::mutate(type_count = n_distinct(type)) %>% + dplyr::ungroup() %>% + dplyr::filter(strain_count >= threshold_count | type_count >= threshold_count) sensitivity_S_pneumoniae_infant_strain %<>% dplyr::mutate(study = factor(study, levels = studies_by_size[studies_by_size %in% unique(sensitivity_S_pneumoniae_infant_strain$study)])) @@ -1371,5 +1690,10 @@ sensitivity_bf_comparison %>% kableExtra::kable() %>% kableExtra::kable_styling(latex_options = "scale_down") +write.csv(bf_comparison, + file = "child_strain_bf_sensitivity_comparison.csv", + quote = FALSE, + row.names = FALSE) + ``` diff --git a/examples/s-pneumoniae-strain-invasiveness.html b/examples/s-pneumoniae-strain-invasiveness.html index 2562c89..273363a 100644 --- a/examples/s-pneumoniae-strain-invasiveness.html +++ b/examples/s-pneumoniae-strain-invasiveness.html @@ -14,230 +14,9 @@ S. pneumoniae strain invasiveness - - + + + + @@ -542,119 +143,12 @@

S. pneumoniae strain invasiveness

-
# Load dependencies
-require(tidyverse)
-#> Loading required package: tidyverse
-#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
-#> ✓ ggplot2 3.3.5     ✓ purrr   0.3.4
-#> ✓ tibble  3.1.3     ✓ dplyr   1.0.7
-#> ✓ tidyr   1.1.3     ✓ stringr 1.4.0
-#> ✓ readr   1.4.0     ✓ forcats 0.5.1
-#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
-#> x dplyr::filter() masks stats::filter()
-#> x dplyr::lag()    masks stats::lag()
-require(magrittr)
-#> Loading required package: magrittr
-#> 
-#> Attaching package: 'magrittr'
-#> The following object is masked from 'package:purrr':
-#> 
-#>     set_names
-#> The following object is masked from 'package:tidyr':
-#> 
-#>     extract
-require(rstan)
-#> Loading required package: rstan
-#> Loading required package: StanHeaders
-#> rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
-#> For execution on a local, multicore CPU with excess RAM we recommend calling
-#> options(mc.cores = parallel::detectCores()).
-#> To avoid recompilation of unchanged Stan programs, we recommend calling
-#> rstan_options(auto_write = TRUE)
-#> 
-#> Attaching package: 'rstan'
-#> The following object is masked from 'package:magrittr':
-#> 
-#>     extract
-#> The following object is masked from 'package:tidyr':
-#> 
-#>     extract
-require(bridgesampling)
-#> Loading required package: bridgesampling
-require(loo)
-#> Loading required package: loo
-#> This is loo version 2.4.1
-#> - Online documentation and vignettes at mc-stan.org/loo
-#> - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
-#> 
-#> Attaching package: 'loo'
-#> The following object is masked from 'package:rstan':
-#> 
-#>     loo
-require(cowplot)
-#> Loading required package: cowplot
-require(ggrepel)
-#> Loading required package: ggrepel
-require(xlsx)
-#> Loading required package: xlsx
-require(gtools)
-#> Loading required package: gtools
-# Load stan package
-library(progressionEstimation)
-pkgbuild::compile_dll()
-roxygen2::roxygenize(package.dir = "..")
-#> ℹ Loading progressionEstimation
-#> Loading required package: kableExtra
-#> 
-#> Attaching package: 'kableExtra'
-#> The following object is masked from 'package:dplyr':
-#> 
-#>     group_rows
-#> Writing NAMESPACE
-#> Writing NAMESPACE
-
-# Define serotype categories and palettes
-vaccine_types <- list(
-  "PCV7" = c("4","6B","9V","14","18C","19F","23F"),
-  "PCV10" = c("1","5","7F"),
-  "PCV13" = c("6A","3","19A"),
-  "PCV15" = c("22F","33F"),
-  "PCV20" = c("8","10A","11A","12F","15B/C"),
-  "PPV23" = c("2","9N","17F","20")
-)
-
-vaccine_colours <- c("No PCV" = "blue",
-                     "PCV7" = "red",
-                     "PCV10" = "orange",
-                     "PCV13" = "coral2",
-                     "PCV15" = "pink",
-                     "PCV20" = "purple",
-                     "PPV23" = "black")
-
-epi_colors <- c(
-  "carriage" = "skyblue",
-  "disease" = "cornflowerblue"
-)
-
-model_name_labels <-
-  c(
-    "type-specific Poisson",
-    "type-specific negative binomial",
-    "strain-specific Poisson",
-    "strain-specific negative binomial",
-    "type-specific strain-modified Poisson",
-    "type-specific strain-modified negative binomial",
-    "strain-specific type-modified Poisson",
-    "strain-specific type-modified negative binomial",
-    "strain- and type-specific Poisson",
-    "strain- and type-specific negative binomial"
-  )

Description and filtering of the dataset

The dataset used in this analysis is contained in the S_pneumoniae_infant_strain object, which includes data from 6 studies on 62 serotypes. The distribution of samples between each study can be plotted, if they are ranked by the mean number of carriage and disease isolates:

The total number of observations for each serotype can be similarly plotted:

-

As many of these serotypes are rare, to facilitate model fitting, we exclude any serotype for which the maximum number of observations is below five:

-

This filtered dataset comprises 38 serotypes.

+

As many of these serotypes are rare, to facilitate model fitting, we exclude any serotype for which the maximum number of observations is below five, and any serotype found in fewer than five strains, and any strain associated with fewer than five serotypes:

+

This filtered dataset comprises 66 isolates of 11 serotypes, 35 strains, and 46 strain-serotype combinations.

Fitting the statistical models

@@ -666,578 +160,376 @@

Fitting the statistical models

\[d_{i,j,k} \sim Poisson(\delta_{i}\nu_{k}\rho_{i,j,k}N_{i}t_{i})\]

We can also fit a negative binomial equivalent (adjusted strain-specific negative binomial model):

\[d_{i,j,k} \sim NegBin(\delta_{i}\nu_{k}\rho_{i,j,k}N_{i}t_{i})\]

-

Models can also combine serotype and strain information, with invasiveness primarily determined by serotype, and modified by strain:

+

Models can also combine serotype and strain information, with invasiveness primarily determined by serotype, and modified by strain:

\[d_{i,j,k} \sim Poisson(\delta_{i}\nu_{k}\nu_{k}\rho_{i,j,k}N_{i}t_{i})\]

This can also be applied using a negative binomial distribution:

\[d_{i,j,k} \sim NegBin(\delta_{i}\nu_{k}\nu_{k}\rho_{i,j,k}N_{i}t_{i})\]

-

Models can alternative have invasiveness primarily determined by strain, and modified by serotype:

+

Models can alternative have invasiveness primarily determined by strain, and modified by serotype:

\[d_{i,j,k} \sim Poisson(\delta_{i}\nu_{k}\nu_{k}\rho_{i,j,k}N_{i}t_{i})\]

This model can also be applied using a negative binomial model:

\[d_{i,j,k} \sim NegBin(\delta_{i}\nu_{k}\nu_{k}\rho_{i,j,k}N_{i}t_{i})\]

-

The final model structure assigns a different invasiveness to each strain-serotype combination:

+

The final model structure assigns a different invasiveness to each strain-serotype combination:

\[d_{i,j,k} \sim Poisson(\delta_{i}\nu_{j,k}\rho_{i,j,k}N_{i}t_{i})\]

A version using the negative binomial distribution can also be fitted:

\[d_{i,j,k} \sim NegBin(\delta_{i}\nu_{j,k}\rho_{i,j,k}N_{i}t_{i})\]

To check the models have fitted correctly, we can plot the \(\hat{R}\) values across MCMCs:

-

-fit_list <- list(adjusted_serotype_specific_poisson_fit,
-                                  adjusted_serotype_specific_negbin_fit,
-                                  adjusted_strain_specific_poisson_fit,
-                                  adjusted_strain_specific_negbin_fit,
-                                  adjusted_serotype_specific_strain_modified_poisson_fit,
-                                  adjusted_strain_specific_strain_modified_negbin_fit,
-                                  adjusted_strain_specific_serotype_modified_poisson_fit,
-                                  adjusted_strain_specific_serotype_modified_negbin_fit,
-                                  adjusted_strain_and_serotype_specific_poisson_fit,
-                                  adjusted_strain_and_serotype_specific_negbin_fit)
-
-rhat_plot <- function(fit) {
-  rhat_plot <- plot(fit, plotfun = "rhat", binwidth = 0.00005)
-  rhat_plot <- rhat_plot + theme(axis.text.x = element_text(angle = 90))
-}
-
-rhat_plots <- lapply(fit_list, rhat_plot)
-
-(strain_and_serotype_rhat_plots <-
-  cowplot::plot_grid(plotlist = rhat_plots, ncol = 5, nrow = 2, labels = "AUTO")
-)
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-#> Warning: Removed 5 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 5 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 5 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 5 rows containing non-finite values (stat_bin).
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-

-

-ggsave(strain_and_serotype_rhat_plots,
-       file = "strain_and_serotype_rhat_plots.png",
-       width = 11,
-       height = 7
-)
+

+fit_list <- list(adjusted_serotype_specific_poisson_fit,
+                                  adjusted_serotype_specific_negbin_fit,
+                                  adjusted_strain_specific_poisson_fit,
+                                  adjusted_strain_specific_negbin_fit,
+                                  adjusted_serotype_specific_strain_modified_poisson_fit,
+                                  adjusted_strain_specific_strain_modified_negbin_fit,
+                                  adjusted_strain_specific_serotype_modified_poisson_fit,
+                                  adjusted_strain_specific_serotype_modified_negbin_fit,
+                                  adjusted_strain_and_serotype_specific_poisson_fit,
+                                  adjusted_strain_and_serotype_specific_negbin_fit)
+
+rhat_plot <- function(fit) {
+  rhat_plot <- plot(fit, plotfun = "rhat", binwidth = 0.00005)
+  rhat_plot <- rhat_plot + theme(axis.text.x = element_text(angle = 90))
+}
+
+rhat_plots <- lapply(fit_list, rhat_plot)
+
+(strain_and_serotype_rhat_plots <-
+  cowplot::plot_grid(plotlist = rhat_plots, ncol = 5, nrow = 2, labels = "AUTO")
+)
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+#> Warning: Removed 5 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 5 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 5 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 5 rows containing non-finite values (stat_bin).
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+
+#> Warning: Removed 3 rows containing non-finite values (stat_bin).
+

+

+ggsave(strain_and_serotype_rhat_plots,
+       file = "strain_and_serotype_rhat_plots.png",
+       width = 11,
+       height = 7
+)

Convergence can also be checked using trace plots of the log likelihood values:

-

-plot_lp <- function(fit) {
-  pl <- rstan::traceplot(fit, pars = "lp__")
-  no_leg_pl <- pl + theme(legend.position = "none",
-                          axis.text.x = element_text(angle = 90))
-  return(no_leg_pl)
-}
-
-trace_plots <- lapply(fit_list, plot_lp)
-
-(strain_and_serotype_trace_plots <-
-  cowplot::plot_grid(plotlist = trace_plots, ncol = 5, nrow = 2, labels = "AUTO")
-)
-

-

-ggsave(strain_and_serotype_trace_plots,
-       file = "strain_and_serotype_trace_plots.png",
-       width = 11,
-       height = 7
-)
+

+plot_lp <- function(fit) {
+  pl <- rstan::traceplot(fit, pars = "lp__")
+  no_leg_pl <- pl + theme(legend.position = "none",
+                          axis.text.x = element_text(angle = 90))
+  return(no_leg_pl)
+}
+
+trace_plots <- lapply(fit_list, plot_lp)
+
+(strain_and_serotype_trace_plots <-
+  cowplot::plot_grid(plotlist = trace_plots, ncol = 5, nrow = 2, labels = "AUTO")
+)
+

+

+ggsave(strain_and_serotype_trace_plots,
+       file = "strain_and_serotype_trace_plots.png",
+       width = 11,
+       height = 7
+)

Compare model observations and predictions

For each model, the output can be processed, and the observations plotted against each model’s predictions.

-

-model_outputs <- list(
-  adjusted_serotype_specific_poisson_output_df,
-  adjusted_serotype_specific_negbin_output_df,
-  adjusted_strain_specific_poisson_output_df,
-  adjusted_strain_specific_negbin_output_df,
-  adjusted_serotype_specific_strain_modified_poisson_output_df,
-  adjusted_serotype_specific_strain_modified_negbin_output_df,
-  adjusted_strain_specific_serotype_modified_poisson_output_df,
-  adjusted_strain_specific_serotype_modified_negbin_output_df,
-  adjusted_strain_and_serotype_specific_poisson_output_df,
-  adjusted_strain_and_serotype_specific_negbin_output_df
-)
-
-label_list <- list(
-  "type",
-  "type",
-  "type",
-  "type",
-  "type",
-  "type",
-  "type",
-  "type",
-  "combined",
-  "combined"
-)
-
-prediction_plots <- list()
-for (i in 1:length(model_outputs)) {
-  prediction_plots[[i]] <- progressionEstimation::plot_case_carrier_predictions(
-                                                       model_outputs[[i]],
-                                                       label_col = label_list[[i]],
-                                                       legend = FALSE,
-                                                       n_label = 0)
-}
-
-no_leg_plot <- cowplot::plot_grid(plotlist = prediction_plots,
-                                  ncol = 1,
-                                  nrow = 8,
-                                  labels = "AUTO",
-                                  vjust = -0.01) +
-      theme(plot.margin = unit(c(0.5,0,0,0), "cm"))
-
-prediction_plot_legend <- progressionEstimation::plot_case_carrier_predictions(model_outputs[[1]], just_legend = TRUE)
-
-pred_v_obs_plot <- 
-  cowplot::plot_grid(no_leg_plot,
-                     prediction_plot_legend,
-                     ncol = 1,
-                     rel_heights = c(1,0.1))
-
-ggsave(pred_v_obs_plot,
-       file = "infant_strain_serotypes_pred_v_obs_plot.png",
-       height = 20,
-       width = 10)
+

+model_outputs <- list(
+  adjusted_serotype_specific_poisson_output_df,
+  adjusted_serotype_specific_negbin_output_df,
+  adjusted_strain_specific_poisson_output_df,
+  adjusted_strain_specific_negbin_output_df,
+  adjusted_serotype_specific_strain_modified_poisson_output_df,
+  adjusted_serotype_specific_strain_modified_negbin_output_df,
+  adjusted_strain_specific_serotype_modified_poisson_output_df,
+  adjusted_strain_specific_serotype_modified_negbin_output_df,
+  adjusted_strain_and_serotype_specific_poisson_output_df,
+  adjusted_strain_and_serotype_specific_negbin_output_df
+)
+
+label_list <- list(
+  "type",
+  "type",
+  "type",
+  "type",
+  "type",
+  "type",
+  "type",
+  "type",
+  "combined",
+  "combined"
+)
+
+prediction_plots <- list()
+for (i in 1:length(model_outputs)) {
+  prediction_plots[[i]] <- progressionEstimation::plot_case_carrier_predictions(
+                                                       model_outputs[[i]],
+                                                       label_col = label_list[[i]],
+                                                       legend = FALSE,
+                                                       n_label = 0)
+}
+
+no_leg_plot <- cowplot::plot_grid(plotlist = prediction_plots,
+                                  ncol = 1,
+                                  nrow = 8,
+                                  labels = "AUTO",
+                                  vjust = -0.01) +
+      theme(plot.margin = unit(c(0.5,0,0,0), "cm"))
+
+prediction_plot_legend <- progressionEstimation::plot_case_carrier_predictions(model_outputs[[1]], just_legend = TRUE)
+
+(pred_v_obs_plot <- 
+  cowplot::plot_grid(no_leg_plot,
+                     prediction_plot_legend,
+                     ncol = 1,
+                     rel_heights = c(1,0.1)))
+

+

+ggsave(pred_v_obs_plot,
+       file = "infant_strain_serotypes_pred_v_obs_plot.png",
+       height = 20,
+       width = 10)

The deviation of the predicted and observed values can be simply evaluated using the root mean square error:

-

-obs_pred_df <-
-  dplyr::bind_rows(model_outputs) %>%
-  dplyr::select(model_name,carriage_rmse,disease_rmse,phi,phi_lower,phi_upper) %>%
-  tidyr::pivot_longer(c(carriage_rmse,disease_rmse), names_to = "Observation", values_to = "RMSE") %>%
-  dplyr::mutate(model_name = factor(model_name,
-                                    levels = c(
-                                      "serotype_specific_poisson",
-                                      "serotype_specific_negbin",
-                                      "strain_specific_poisson",
-                                      "strain_specific_negbin",
-                                      "serotype_specific_strain_modified_poisson",
-                                      "serotype_specific_strain_modified_negbin",
-                                      "strain_specific_serotype_modified_poisson",
-                                      "strain_specific_serotype_modified_negbin",
-                                      "strain_and_serotype_specific_poisson",
-                                      "strain_and_serotype_specific_negbin"
-                                      )
-                                    )
-                ) %>%
-  dplyr::mutate(Observation = dplyr::case_when(
-                    Observation == "carriage_rmse" ~ "Carriage",
-                    Observation == "disease_rmse" ~ "Disease"
-                  )
-                )
-
-(strain_and_serotype_rmse_plot <-
-  ggplot(obs_pred_df, aes(x = model_name, y = RMSE)) +
-    geom_point(position = position_jitter(width = 0.25),
-               alpha = 0.25,
-               cex = 0.75,
-               colour = "blue",
-               pch = 4) +
-    geom_violin(fill = NA) +
-    scale_y_continuous(trans="log10") +
-    xlab("Model name") +
-    scale_x_discrete(labels = model_name_labels) +
-    theme_bw() +
-    facet_grid(Observation ~ .) +
-    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
-)
-

-

-ggsave(strain_and_serotype_rmse_plot,
-       file = "strain_and_serotype_rmse_plot.png",
-       width = 7,
-       height = 7
-)
+

+obs_pred_df <-
+  dplyr::bind_rows(model_outputs) %>%
+  dplyr::select(model_name,carriage_rmse,disease_rmse,phi,phi_lower,phi_upper) %>%
+  tidyr::pivot_longer(c(carriage_rmse,disease_rmse), names_to = "Observation", values_to = "RMSE") %>%
+  dplyr::mutate(model_name = factor(model_name,
+                                    levels = c(
+                                      "serotype_specific_poisson",
+                                      "serotype_specific_negbin",
+                                      "strain_specific_poisson",
+                                      "strain_specific_negbin",
+                                      "serotype_specific_strain_modified_poisson",
+                                      "serotype_specific_strain_modified_negbin",
+                                      "strain_specific_serotype_modified_poisson",
+                                      "strain_specific_serotype_modified_negbin",
+                                      "strain_and_serotype_specific_poisson",
+                                      "strain_and_serotype_specific_negbin"
+                                      )
+                                    )
+                ) %>%
+  dplyr::mutate(Observation = dplyr::case_when(
+                    Observation == "carriage_rmse" ~ "Carriage",
+                    Observation == "disease_rmse" ~ "Disease"
+                  )
+                )
+
+(strain_and_serotype_rmse_plot <-
+  ggplot(obs_pred_df, aes(x = model_name, y = RMSE)) +
+    geom_point(position = position_jitter(width = 0.25),
+               alpha = 0.25,
+               cex = 0.75,
+               colour = "blue",
+               pch = 4) +
+    geom_violin(fill = NA) +
+    scale_y_continuous(trans="log10") +
+    xlab("Model name") +
+    scale_x_discrete(labels = model_name_labels) +
+    theme_bw() +
+    facet_grid(Observation ~ .) +
+    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+)
+

+

+ggsave(strain_and_serotype_rmse_plot,
+       file = "strain_and_serotype_rmse_plot.png",
+       width = 7,
+       height = 7
+)

The fits of the negative binomial can be evaluated through plotting the estimates of the precision parameter, \(\phi\). As \(\phi\) increases, the variance of the negative binomial distribution decreases, and the negative binomal model becomes more similar to the Poisson model.

-

-(strain_and_serotype_precision_parameters <-
-  ggplot(obs_pred_df %>%
-          dplyr::filter(!is.na(phi)) %>%
-          dplyr::group_by(model_name) %>%
-          dplyr::slice(1) %>%
-          dplyr::ungroup(),
-        aes(x = model_name,
-            y = phi,
-            ymin = phi_lower,
-            ymax = phi_upper)) +
-    geom_point() +
-    geom_errorbar(width = 0.25) +
-    theme_bw() +
-    scale_y_continuous(trans="log10") +
-    ylab(expression(phi)) +
-    xlab("Model name") +
-    scale_x_discrete(labels = model_name_labels[c(2,4,6,8,10)]) +
-    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
-)
-

-

-ggsave(strain_and_serotype_precision_parameters,
-       file = "strain_and_serotype_precision_plot.png",
-       width = 6,
-       height = 6
-)
+

+(strain_and_serotype_precision_parameters <-
+  ggplot(obs_pred_df %>%
+          dplyr::filter(!is.na(phi)) %>%
+          dplyr::group_by(model_name) %>%
+          dplyr::slice(1) %>%
+          dplyr::ungroup(),
+        aes(x = model_name,
+            y = phi,
+            ymin = phi_lower,
+            ymax = phi_upper)) +
+    geom_point() +
+    geom_errorbar(width = 0.25) +
+    theme_bw() +
+    scale_y_continuous(trans="log10") +
+    ylab(expression(phi)) +
+    xlab("Model name") +
+    scale_x_discrete(labels = model_name_labels[c(2,4,6,8,10)]) +
+    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+)
+

+

+ggsave(strain_and_serotype_precision_parameters,
+       file = "strain_and_serotype_precision_plot.png",
+       width = 6,
+       height = 6
+)
+
+
+

Plot secondary invasiveness for modified invasiveness models

+

To check these are not being constrained by the prior limits, we plot the invasiveness modification values, first for the type-specific strain-modified Poisson model:

+

+order_strains <-
+  model_outputs[[5]] %>%
+    dplyr::select(strain,secondary_nu) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(secondary_nu)) %>%
+    dplyr::select(strain) %>%
+    dplyr::mutate(strain = as.character(strain)) %>%
+    dplyr::pull()
+
+(strain_inv <-
+  progressionEstimation::plot_progression_rates(model_outputs[[5]] %>%
+                                                  dplyr::mutate(strain = factor(strain,
+                                                                                levels = order_strains)),
+                                                type = "strain"))
+

+

+ggsave(strain_inv,
+       file = "type_specific_strain_modified_strain_invasiveness.png",
+       width = 8,
+       height = 6)
+

+progressionEstimation::plot_progression_rates(model_outputs[[6]], type = "strain")
+

+

+progressionEstimation::plot_progression_rates(model_outputs[[7]])
+

+

+progressionEstimation::plot_progression_rates(model_outputs[[8]])
+

Run model comparison with leave-one-out cross-validation

The model likelihoods can be compared using leave-one-out cross-validation:

-

The Pareto distribution k values are too high for robust estimates of the ELPD. This reflects many of the points being

-
-
-

Run model comparison with Bayes factors

-

As the models can instead be compared with Bayes factors:

-
-
-

Plot serotype invasiveness

-

The best-fitting model can then be applied to the overall dataset.

-

-full_infant_serotype_and_strain_invasiveness <- 
-  progressionEstimation::process_input_data(S_pneumoniae_infant_strain,
-                                            combine_strain = TRUE,
-                                            condense = FALSE)
-
-full_adjusted_strain_and_serotype_specific_poisson_fit <- 
-  progressionEstimation::fit_progression_rate_model(full_infant_serotype_and_strain_invasiveness,
-                                                    type_specific = TRUE,
-                                                    location_adjustment = TRUE,
-                                                    stat_model = "poisson",
-                                                    model_description = "strain_and_serotype_specific_poisson",
-                                                    num_chains = n_chains,
-                                                    num_iter = n_iter,
-                                                    num_cores = n_core,
-                                                    adapt_delta_value = adapt_delta,
-                                                    stepsize_value = stepsize,
-                                                    max_treedepth_value = max_treedepth)
-
-rhat_plot <- plot(full_adjusted_strain_and_serotype_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005)
-
-trace_plot <- rstan::traceplot(full_adjusted_strain_and_serotype_specific_poisson_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90))
-
-(full_strain_and_serotype_validation_plot <-
-  cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
-                     nrow = 1,
-                     ncol = 2,
-                     labels = "AUTO")
-)
-#> Warning: Removed 3 rows containing non-finite values (stat_bin).
-

-

-ggsave(full_strain_and_serotype_validation_plot,
-       file = "full_strain_and_serotype_validation_plot.png",
-       width = 7,
-       height = 5
-)
-

-# Annotate serotypes by status
-best_fitting_output <- 
-  progressionEstimation::process_progression_rate_model_output(full_adjusted_strain_and_serotype_specific_poisson_fit,
-                                                               S_pneumoniae_infant_strain,
-                                                               combined_strain_type = TRUE) %>%
-    dplyr::mutate("type" = S_pneumoniae_infant_strain$type) %>%
-    dplyr::mutate("classification" = dplyr::case_when(
-        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
-        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
-        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
-        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
-        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
-        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
-        TRUE ~ "No PCV"
-      )
-    ) %>%
-    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
-                                                                     "PCV10",
-                                                                     "PCV13",
-                                                                     "PCV15",
-                                                                     "PCV20",
-                                                                     "PPV23",
-                                                                     "No PCV")))
-
-# Order serotypes
-strains_by_invasiveness <-
-  best_fitting_output %>%
-    dplyr::select(combined,nu) %>%
-    dplyr::distinct() %>%
-    dplyr::arrange(desc(nu)) %>%
-    dplyr::select(combined) %>%
-    dplyr::pull()
-
-best_fitting_output %<>%
-  dplyr::mutate(combined = factor(combined, levels = strains_by_invasiveness))
-
-# Plot
-(full_invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(best_fitting_output,
-                                                type = "combined",
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE) +
-    theme(axis.text.x = element_text(size = 6))
-)
-

-

-ggsave(full_invasiveness_plot,
-       file = "full_strain_and_serotype_invasiveness_plot.png",
-       width = 20,
-       height = 10
-)
-
-
-

Save overall dataset

-
 
-write.csv(best_fitting_output %>%
-            dplyr::select(combined,nu,nu_lower,nu_upper) %>%
-            dplyr::rename(genotype = combined) %>%
-            dplyr::rename(invasiveness = nu) %>%
-            dplyr::rename(invasiveness_lower = nu_lower) %>%
-            dplyr::rename(invasiveness_upper = nu_upper) %>%
-            dplyr::distinct(),
-          file = "Dataset_S3.csv",
-          quote = F,
-          row.names = F)
-
-
-

Filter to only larger sample sizes

-

-# Annotate sample size
-best_fitting_output %<>%
-  dplyr::group_by(combined) %>%
-  dplyr::mutate(num_observations = sum(carriage+disease)) %>%
-  dplyr::ungroup() %>%
-  dplyr::filter(num_observations >= 10) %>%
-  dplyr::group_by(strain) %>%
-  dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>%
-  dplyr::ungroup() %>%
-  dplyr::group_by(type) %>%
-  dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>%
-  dplyr::ungroup()
-
-# Plot
-(invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(best_fitting_output,
-                                                type = "combined",
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE))
-

-

-mixedrank = function(x) order(gtools::mixedorder(as.character(x)))
-
-# Reorder by serotype
-strain_and_serotype_levels <-
-  best_fitting_output %>%
-    dplyr::select(combined,classification) %>%
-    dplyr::distinct() %>%
-    dplyr::arrange(classification,combined) %>%
-    dplyr::select(combined) %>%
-    dplyr::pull()
-
-serotype_levels <-
-  best_fitting_output %>%
-    dplyr::select(type,classification) %>%
-    dplyr::distinct() %>%
-    dplyr::group_by(classification) %>%
-    dplyr::arrange(mixedrank(type),
-                   .by_group = TRUE) %>%
-    dplyr::ungroup() %>%
-    dplyr::select(type) %>%
-    dplyr::pull()
-
-best_fitting_output %<>%
-  dplyr::mutate(combined = factor(combined, levels = strain_and_serotype_levels)) %>%
-  dplyr::mutate(type = factor(type, levels = serotype_levels))
-
-(serotype_invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(best_fitting_output %>%
-                                                  dplyr::filter(num_strains > 1),
-                                                type = "combined",
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE) +
-                                                facet_wrap(.~type,
-                                                           scales = 'free_x'))
-

-

-ggsave(serotype_invasiveness_plot,
-       file = "within_serotype_invasiveness_variation_plot.png",
-       width = 8,
-       height = 12
-)
-

-strain_levels <-
-  best_fitting_output %>%
-    dplyr::select(strain) %>%
-    dplyr::distinct() %>%
-    dplyr::arrange(mixedrank(strain)) %>%
-    dplyr::pull()
-
-best_fitting_output %<>%
-  dplyr::mutate(strain = factor(strain, levels = strain_levels))
-
-(strain_invasiveness_plot <-
-  progressionEstimation::plot_progression_rates(best_fitting_output %>%
-                                                  dplyr::filter(num_serotypes > 1),
-                                                type = "combined",
-                                                unit_time = "year",
-                                                type_name = "Serotype",
-                                                colour_col = "classification",
-                                                colour_palette = vaccine_colours,
-                                                use_sample_size = TRUE) +
-                                                facet_wrap(.~strain,
-                                                           scales = 'free_x'))
-

-

-ggsave(strain_invasiveness_plot,
-       file = "within_strain_invasiveness_variation_plot.png",
-       width = 8,
-       height = 8
-)
-
-
-

Plot study-specific scale factors

-

-(scale_factor_plot <-
-  progressionEstimation::plot_study_scale_factors(best_fitting_output))
-

-

-ggsave(scale_factor_plot,
-       file = "full_strain_and_serotype_scale_factor_plot.png",
-       width = 6,
-       height = 6
-)
-

-sensitivity_S_pneumoniae_infant_strain <-
-  S_pneumoniae_infant_strain %>%
-    dplyr::filter(carriage >= threshold_count | disease >= threshold_count) %>%
-    dplyr::mutate(carriage_samples = dplyr::case_when(
-                      study %in% c("Finland.Pre.PCV","Oxford.pre.PCV","Stockholm.pre.PCV") ~ as.integer(carriage_samples*100),
-                      TRUE ~ carriage_samples
-                    )
-                  )
-
-sensitivity_S_pneumoniae_infant_strain %<>%
-    dplyr::mutate(study = factor(study, levels = studies_by_size[studies_by_size %in% unique(sensitivity_S_pneumoniae_infant_strain$study)]))
-
-sensitivity_S_pneumoniae_infant_strain %<>%
-    dplyr::mutate(type = factor(type,
-                                          levels = serotype_by_count[serotype_by_count %in% unique(sensitivity_S_pneumoniae_infant_strain$type)])) %>%
-  dplyr::mutate(strain = factor(strain))
-
-# Generate input for serotype models
-sensitivity_infant_serotype_invasiveness <- 
-  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
-                                            condense = FALSE)
-
-# Generate input for strain models
-sensitivity_infant_strain_invasiveness <- 
-  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
-                                            type = "strain",
-                                            condense = FALSE)
-
-# Generate input for strain and serotype models
-sensitivity_infant_serotype_and_strain_invasiveness <- 
-  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
-                                            use_strain = TRUE,
-                                            condense = FALSE)
-
-# Generate input for serotype models
-sensitivity_infant_serotype_strain_combined_invasiveness <- 
-  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
-                                            combine_strain = TRUE,
-                                            condense = FALSE)
-

Fit the first model:

-
sensitivity_adjusted_serotype_specific_poisson_fit <- 
-  progressionEstimation::fit_progression_rate_model(sensitivity_infant_serotype_invasiveness,
-                                                    type_specific = TRUE,
-                                                    location_adjustment = TRUE,
-                                                    stat_model = "poisson",
-                                                    model_description = "serotype_specific_poisson",
-                                                    num_chains = n_chains,
-                                                    num_iter = n_iter,
-                                                    num_cores = n_core,
-                                                    adapt_delta_value = adapt_delta,
-                                                    stepsize_value = stepsize,
-                                                    max_treedepth_value = max_treedepth)
-
-sensitivity_adjusted_serotype_specific_poisson_output_df <-
-  progressionEstimation::process_progression_rate_model_output(sensitivity_adjusted_serotype_specific_poisson_fit,
-                                                               sensitivity_S_pneumoniae_infant_strain,
-                                                               condense = FALSE)
-

-sensitivity_fit_list <- list(
-  sensitivity_adjusted_serotype_specific_poisson_fit,
-  sensitivity_adjusted_serotype_specific_negbin_fit,
-  sensitivity_adjusted_strain_specific_poisson_fit,
-  sensitivity_adjusted_strain_specific_negbin_fit,
-  sensitivity_adjusted_serotype_specific_strain_modified_poisson_fit,
-  sensitivity_adjusted_strain_specific_strain_modified_negbin_fit,
-  sensitivity_adjusted_strain_specific_serotype_modified_poisson_fit,
-  sensitivity_adjusted_strain_specific_serotype_modified_negbin_fit,
-  sensitivity_adjusted_strain_and_serotype_specific_poisson_fit,
-  sensitivity_adjusted_strain_and_serotype_specific_negbin_fit
-)
-
-sensitivity_bf_comparison <- 
-  progressionEstimation::compare_model_fits_with_bf(
-                                                    sensitivity_fit_list,
-                                                    num_iter = n_iter,
-                                                    num_threads = n_core)
-
-sensitivity_bf_comparison %>%
-  kableExtra::kable()  %>%
-  kableExtra::kable_styling(latex_options = "scale_down")
+

+loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list,
+                                                                     use_moments = FALSE,
+                                                                     num_threads = n_core)
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+loo_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + - - - - - - + + + + + + + + + + @@ -1245,23 +537,86 @@

Plot study-specific scale factors

strain_specific_serotype_modified_poisson + + + + + + + + + + + + + + + + + + + + + @@ -1269,27 +624,1172 @@

Plot study-specific scale factors

serotype_specific_negbin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-Model -log_Bayes_factor +elpd_diff + +se_diff + +elpd_loo + +se_elpd_loo + +p_loo + +se_p_loo + +looic + +se_looic
-strain_and_serotype_specific_poisson +serotype_specific_strain_modified_poisson -0.00000 +0.000000
-serotype_specific_poisson + +0.000000 --77.47534 +-385.2019
-strain_specific_poisson + +9.800251 + +94.92273 + +3.092583 --86.11976 +770.4039 + +19.60050
-serotype_specific_strain_modified_poisson +strain_and_serotype_specific_poisson + +-1.555928 + +3.565421 + +-386.7579 + +10.780299 + +99.91711 + +3.609332 --128.05953 +773.5157 + +21.56060
--132.60635 +-4.769573 + +3.497835 + +-389.9715 + +10.265235 + +101.69951 + +3.628416 + +779.9430 + +20.53047
-strain_and_serotype_specific_negbin +serotype_specific_strain_modified_negbin + +-26.972372 + +3.337377 + +-412.1743 + +11.260456 + +91.87327 + +3.011936 + +824.3486 --260.16672 +22.52091
-strain_specific_negbin +strain_specific_serotype_modified_negbin + +-37.882645 + +4.894518 + +-423.0846 + +12.244943 + +100.39207 + +3.504499 + +846.1692 --296.47068 +24.48989
--314.80174 +-41.081348 + +5.905017 + +-426.2833 + +12.486938 + +81.70653 + +2.927903 + +852.5666 + +24.97388
-serotype_specific_strain_modified_negbin +strain_specific_poisson --390.64244 +-43.612212 + +18.761103 + +-428.8142 + +22.254472 + +116.78620 + +11.304089 + +857.6283 + +44.50894
-strain_specific_serotype_modified_negbin +serotype_specific_poisson + +-45.209309 + +14.483087 + +-430.4113 + +18.829471 + +94.04073 + +6.146281 + +860.8225 + +37.65894 +
+strain_and_serotype_specific_negbin + +-48.226987 + +6.016410 + +-433.4289 + +12.750154 + +108.09451 + +3.724335 + +866.8579 + +25.50031 +
+strain_specific_negbin + +-61.001578 + +6.806206 + +-446.2035 + +13.067118 + +103.22326 + +3.351319 + +892.4070 + +26.13424 +
+

+write.csv(loo_comparison,
+          file = "child_strain_loo_comparison.csv",
+          quote = FALSE,
+          row.names = TRUE)
+

The Pareto distribution k values are too high for robust estimates of the ELPD. This reflects there being too few observations per parameter for this type of evaluation. Even usingt the disease likelihoods, we cannot calculate an accuraste cross-validation:

+

+disease_loo_comparison <- progressionEstimation::compare_model_fits_with_loo(fit_list,
+                                                                     log_lik_param = "disease_log_lik",
+                                                                     use_moments = FALSE,
+                                                                     num_threads = n_core)
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
+disease_loo_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +elpd_diff + +se_diff + +elpd_loo + +se_elpd_loo + +p_loo + +se_p_loo + +looic + +se_looic +
+serotype_specific_strain_modified_poisson + +0.0000000 + +0.000000 + +-175.2046 + +8.394341 + +43.54962 + +3.167350 + +350.4093 + +16.78868 +
+strain_and_serotype_specific_poisson + +-0.5731933 + +2.656717 + +-175.7778 + +9.143976 + +46.12602 + +3.392953 + +351.5556 + +18.28795 +
+strain_specific_serotype_modified_poisson + +-3.2917825 + +2.344296 + +-178.4964 + +9.074371 + +47.91023 + +3.576116 + +356.9928 + +18.14874 +
+serotype_specific_strain_modified_negbin + +-21.1370237 + +2.476542 + +-196.3416 + +10.043093 + +33.30378 + +2.547575 + +392.6833 + +20.08619 +
+serotype_specific_negbin + +-32.0800347 + +5.135090 + +-207.2847 + +11.417514 + +23.49981 + +3.525347 + +414.5693 + +22.83503 +
+strain_specific_serotype_modified_negbin + +-32.9355456 + +4.169784 + +-208.1402 + +10.986727 + +41.67588 + +3.200970 + +416.2803 + +21.97345 +
+strain_specific_poisson + +-36.8465948 + +15.833223 + +-212.0512 + +18.073692 + +68.13592 + +10.971619 + +424.1024 + +36.14738 +
+strain_and_serotype_specific_negbin + +-41.1717194 + +5.350614 + +-216.3763 + +11.894632 + +46.81588 + +3.660288 + +432.7527 + +23.78926 +
+serotype_specific_poisson + +-44.0438459 + +13.049183 + +-219.2485 + +16.692722 + +67.38613 + +9.936623 + +438.4969 + +33.38544 +
+strain_specific_negbin + +-51.2781587 + +5.626094 + +-226.4828 + +11.745446 + +40.11151 + +3.118328 + +452.9656 + +23.49089 +
+

+write.csv(disease_loo_comparison,
+          file = "child_strain_disease_loo_comparison.csv",
+          quote = FALSE,
+          row.names = TRUE)
+
+
+

Run model comparison with Bayes factors

+

As the models can instead be compared with Bayes factors:

+

+bf_comparison <- progressionEstimation::compare_model_fits_with_bf(fit_list,
+                                                                   num_iter = n_iter,
+                                                                   num_threads = n_core)
+bf_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Model + +log_Bayes_factor +
+serotype_specific_strain_modified_poisson + +0.000000 +
+serotype_specific_negbin + +-5.593207 +
+serotype_specific_strain_modified_negbin + +-5.985671 +
+serotype_specific_poisson + +-24.607137 +
+strain_specific_serotype_modified_poisson + +-25.268827 +
+strain_specific_serotype_modified_negbin + +-29.979446 +
+strain_and_serotype_specific_poisson + +-33.292019 +
+strain_specific_negbin + +-33.940225 +
+strain_and_serotype_specific_negbin + +-37.325861 +
+strain_specific_poisson + +-49.461642 +
+

+write.csv(bf_comparison,
+          file = "child_strain_bf_comparison.csv",
+          quote = FALSE,
+          row.names = FALSE)
+
+
+

Plot serotype invasiveness

+

The best-fitting model can then be applied to the overall dataset.

+

+# Generate input for strain and serotype models
+full_infant_serotype_and_strain_invasiveness <- 
+  progressionEstimation::process_input_data(S_pneumoniae_infant_strain,
+                                            use_strain = TRUE,
+                                            condense = FALSE)
+
+full_adjusted_serotype_specific_strain_modified_poisson_fit <- 
+  progressionEstimation::fit_progression_rate_model(full_infant_serotype_and_strain_invasiveness,
+                                                    type_specific = TRUE,
+                                                    location_adjustment = TRUE,
+                                                    strain_as_secondary_type = TRUE,
+                                                    stat_model = "poisson",
+                                                    model_description = "serotype_specific_strain_modified_poisson",
+                                                    num_chains = n_chains,
+                                                    num_iter = n_iter,
+                                                    num_cores = n_core,
+                                                    adapt_delta_value = adapt_delta,
+                                                    stepsize_value = stepsize,
+                                                    max_treedepth_value = max_treedepth)
+
+rhat_plot <- plot(full_adjusted_serotype_specific_strain_modified_poisson_fit,
+                  plotfun = "rhat",
+                  binwidth = 0.00005)
+
+trace_plot <- rstan::traceplot(full_adjusted_serotype_specific_strain_modified_poisson_fit,
+                               pars = "lp__") +
+              theme(axis.text.x = element_text(angle = 90))
+
+(full_strain_and_serotype_validation_plot <-
+  cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot),
+                     nrow = 1,
+                     ncol = 2,
+                     labels = "AUTO")
+)
+#> Warning: Removed 5 rows containing non-finite values (stat_bin).
+

+

+ggsave(full_strain_and_serotype_validation_plot,
+       file = "full_strain_and_serotype_validation_plot.png",
+       width = 7,
+       height = 5
+)
+

+# Annotate serotypes by status
+best_fitting_output <- 
+  progressionEstimation::process_progression_rate_model_output(full_adjusted_serotype_specific_strain_modified_poisson_fit,
+                                                               S_pneumoniae_infant_strain,
+                                                               strain_as_secondary_type = TRUE,
+                                                               condense = FALSE) %>%
+    dplyr::mutate("type" = S_pneumoniae_infant_strain$type) %>%
+    dplyr::mutate("classification" = dplyr::case_when(
+        type %in% vaccine_types[["PCV7"]] ~ "PCV7",
+        type %in% vaccine_types[["PCV10"]] ~ "PCV10",
+        type %in% vaccine_types[["PCV13"]] ~ "PCV13",
+        type %in% vaccine_types[["PCV15"]] ~ "PCV15",
+        type %in% vaccine_types[["PCV20"]] ~ "PCV20",
+        type %in% vaccine_types[["PPV23"]] ~ "PPV23",
+        TRUE ~ "No PCV"
+      )
+    ) %>%
+    dplyr::mutate(classification = factor(classification, levels = c("PCV7",
+                                                                     "PCV10",
+                                                                     "PCV13",
+                                                                     "PCV15",
+                                                                     "PCV20",
+                                                                     "PPV23",
+                                                                     "No PCV"))) %>%
+    dplyr::mutate(combined_nu = nu * secondary_nu) %>%
+    tidyr::unite(combined,
+                 type,strain,
+                 sep = "_",
+                 remove = FALSE)
+
+# Order serotypes
+serotypes_by_invasiveness <-
+  best_fitting_output %>%
+    dplyr::select(type,nu) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(nu)) %>%
+    dplyr::select(type) %>%
+    dplyr::mutate(type = as.character(type)) %>%
+    dplyr::pull()
+
+# Order strains
+strains_by_invasiveness <-
+  best_fitting_output %>%
+    dplyr::select(strain,secondary_nu) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(secondary_nu)) %>%
+    dplyr::select(strain) %>%
+    dplyr::mutate(strain = as.character(strain)) %>%
+    dplyr::pull()
+
+best_fitting_output %<>%
+  dplyr::mutate(type = factor(type, levels = serotypes_by_invasiveness)) %>%
+  dplyr::mutate(strain = factor(strain, levels = strains_by_invasiveness))
+
+# Plot
+strain_invasiveness <-
+  progressionEstimation::plot_progression_rates(best_fitting_output,
+                                                type = "strain",
+                                                unit_time = "year",
+                                                type_name = "GPSC",
+                                                use_sample_size = TRUE) +
+    ylab("Progression rate contribution\n(disease per carrier per year)") +
+    theme(axis.text.x = element_text(size = 6))
+
+type_invasiveness <-
+  progressionEstimation::plot_progression_rates(best_fitting_output,
+                                                type = "type",
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE) +
+    ylab("Progression rate contribution\n(disease per carrier per year)") +
+    theme(axis.text.x = element_text(size = 6))
+
+(joint_invasiveness <-
+  cowplot::plot_grid(plotlist = list(strain_invasiveness + theme(legend.position = "none"),
+                                     type_invasiveness),
+                     labels = "AUTO",
+                     nrow = 2,
+                     rel_heights = c(1,1.25)))
+

+

+ggsave(joint_invasiveness,
+       file = "full_strain_and_serotype_invasiveness_plot.png",
+       width = 20,
+       height = 10
+)
+

+not_in_current_vaccines <- c("No PCV","PPV23","PCV20","PCV15")
+
+(all_combined_invasiveness <-
+  ggplot(best_fitting_output %>%
+           dplyr::select(combined,combined_nu, classification),
+         aes(x = combined,
+             y = combined_nu,
+             colour = classification,
+             label = combined)) +
+    geom_point() +
+    scale_y_continuous(trans = "log10") +
+    ylab(expression(nu~"(disease per carrier per year)")) +
+    scale_colour_manual(values = vaccine_colours) +
+    xlab("Combined serotype-strain genotype") +
+    theme_bw() +
+    theme(axis.text.x = element_text(angle = 90,
+                                     hjust = 1,
+                                     vjust = 0.5,
+                                     size = 3.5),
+          legend.position = "bottom") +
+    ggrepel::geom_label_repel(data = best_fitting_output %>%
+                                      dplyr::select(combined,combined_nu, classification) %>%
+                                      dplyr::filter(classification %in% not_in_current_vaccines[1:2]) %>%
+                                        dplyr::filter(combined_nu > 10**(-3.25)) %>%
+                                        dplyr::distinct(),
+                              aes(label = combined),
+                              force_pull = 0.0,
+                              force = 10,
+                              direction = "y",
+                              size = 4,
+                              max.overlaps = 20)
+)
+

+

+ggsave(all_combined_invasiveness,
+       file = "combined_invasiveness_for_all_genotypes.png",
+       width = 11,
+       height = 8)
+
+
+

Save overall dataset

+
 
+write.csv(best_fitting_output %>%
+            dplyr::select(combined,type,strain,
+                          nu,nu_lower,nu_upper,
+                          secondary_nu,secondary_nu_lower,secondary_nu_upper) %>%
+            dplyr::rename(genotype = combined) %>%
+            dplyr::rename(serotype_invasiveness = nu) %>%
+            dplyr::rename(serotype_invasiveness_lower = nu_lower) %>%
+            dplyr::rename(serotype_invasiveness_upper = nu_upper) %>%
+            dplyr::rename(strain_invasiveness = secondary_nu) %>%
+            dplyr::rename(strain_invasiveness_lower = secondary_nu_lower) %>%
+            dplyr::rename(strain_invasiveness_upper = secondary_nu_upper) %>%
+            dplyr::distinct() %>%
+            dplyr::arrange(genotype),
+          file = "Dataset_S3.csv",
+          quote = F,
+          row.names = F)
+
+
+

Filter to only larger sample sizes

+

+# Annotate sample size
+filtered_best_fitting_output <-
+  best_fitting_output %>%
+    dplyr::group_by(combined) %>%
+    dplyr::mutate(num_observations = sum(carriage+disease)) %>%
+    dplyr::ungroup() %>%
+    dplyr::filter(num_observations >= 10) %>%
+    dplyr::group_by(strain) %>%
+    dplyr::mutate(num_serotypes = dplyr::n_distinct(type)) %>%
+    dplyr::ungroup() %>%
+    dplyr::group_by(type) %>%
+    dplyr::mutate(num_strains = dplyr::n_distinct(strain)) %>%
+    dplyr::ungroup()
+
+# Plot
+filtered_strain_invasiveness <-
+  progressionEstimation::plot_progression_rates(filtered_best_fitting_output,
+                                                type = "strain",
+                                                unit_time = "year",
+                                                type_name = "GPSC",
+                                                use_sample_size = TRUE) +
+    theme(axis.text.x = element_text(size = 6))
+
+filtered_type_invasiveness <-
+  progressionEstimation::plot_progression_rates(filtered_best_fitting_output,
+                                                type = "type",
+                                                unit_time = "year",
+                                                type_name = "Serotype",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE) +
+    theme(axis.text.x = element_text(size = 6))
+
+(filtered_joint_invasiveness <-
+  cowplot::plot_grid(plotlist = list(filtered_strain_invasiveness + theme(legend.position = "none"),
+                                     filtered_type_invasiveness),
+                     labels = "AUTO",
+                     nrow = 2,
+                     rel_heights = c(1,1.25)))
+

+

+ggsave(filtered_joint_invasiveness,
+       file = "filtered_full_strain_and_serotype_invasiveness_plot.png",
+       width = 20,
+       height = 10
+)
+

+# Function needed if processing combined serotype/strain assignments
+mixedrank = function(x) order(gtools::mixedorder(as.character(x)))
+
+# Reorder by serotype
+serotype_levels <-
+  filtered_best_fitting_output %>%
+    dplyr::select(type,classification) %>%
+    dplyr::distinct() %>%
+    dplyr::group_by(classification) %>%
+    dplyr::arrange(mixedrank(type),
+                   .by_group = TRUE) %>%
+    dplyr::ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::mutate(as.character(type)) %>%
+    dplyr::pull()
+
+# Reorder by strain
+strain_levels <-
+  filtered_best_fitting_output %>%
+    dplyr::select(strain,secondary_nu) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(secondary_nu)) %>%
+    dplyr::select(strain) %>%
+    dplyr::mutate(as.character(strain)) %>%
+    dplyr::pull()
+
+filtered_best_fitting_output %<>%
+  dplyr::mutate(strain = factor(strain, levels = strain_levels)) %>%
+  dplyr::mutate(type = factor(type, levels = serotype_levels))
+
+(serotype_invasiveness_plot <-
+  plot_progression_rate_by_type(filtered_best_fitting_output %>%
+                                                  dplyr::filter(num_strains > 1),
+                                                type = "strain",
+                                                unit_time = "year",
+                                                type_name = "Strain",
+                                                colour_col = "classification",
+                                                colour_palette = vaccine_colours,
+                                                use_sample_size = TRUE) +
+                                                facet_wrap(.~type,
+                                                           scales = 'free_x'))
+

+

+ggsave(serotype_invasiveness_plot,
+       file = "within_serotype_invasiveness_variation_plot.png",
+       width = 8,
+       height = 12
+)
+
+ggsave(serotype_invasiveness_plot,
+       file = "within_serotype_invasiveness_variation_plot.pdf",
+       width = 8,
+       height = 12
+)
+

+# Reorder by serotype
+serotype_levels <-
+  filtered_best_fitting_output %>%
+    dplyr::select(type,nu) %>%
+    dplyr::distinct() %>%
+    dplyr::arrange(desc(nu)) %>%
+    dplyr::ungroup() %>%
+    dplyr::select(type) %>%
+    dplyr::mutate(as.character(type)) %>%
+    dplyr::pull()
+
+# Reorder by strain
+strain_levels <-
+  gtools::mixedsort(
+    filtered_best_fitting_output %>%
+      dplyr::select(strain) %>%
+      dplyr::distinct() %>%
+      dplyr::mutate(strain = as.character(strain)) %>%
+      dplyr::pull()
+    )
+
+filtered_best_fitting_output %<>%
+  dplyr::mutate(strain = factor(strain, levels = strain_levels)) %>%
+  dplyr::mutate(type = factor(type, levels = serotype_levels))
+
+(strain_invasiveness_plot <-
+  plot_progression_rate_by_type(filtered_best_fitting_output %>%
+                                                    dplyr::filter(num_serotypes > 1),
+                                                  type = "type",
+                                                  unit_time = "year",
+                                                  type_name = "Serotype",
+                                                  colour_col = "classification",
+                                                  colour_palette = vaccine_colours,
+                                                  use_sample_size = TRUE) +
+                                                  facet_wrap(.~strain,
+                                                             scales = 'free_x')
+)
+

+

+ggsave(strain_invasiveness_plot,
+       file = "within_strain_invasiveness_variation_plot.png",
+       width = 8,
+       height = 8
+)
+
+ggsave(strain_invasiveness_plot,
+       file = "within_strain_invasiveness_variation_plot.pdf",
+       width = 8,
+       height = 8
+)
+
+
+

Plot study-specific scale factors

+

+(scale_factor_plot <-
+  progressionEstimation::plot_study_scale_factors(best_fitting_output))
+

+

+ggsave(scale_factor_plot,
+       file = "full_strain_and_serotype_scale_factor_plot.png",
+       width = 6,
+       height = 6
+)
+

+sensitivity_S_pneumoniae_infant_strain <-
+  S_pneumoniae_infant_strain %>%
+    dplyr::filter(carriage >= threshold_count | disease >= threshold_count) %>%
+    dplyr::mutate(carriage_samples = dplyr::case_when(
+                      study %in% c("Finland.Pre.PCV","Oxford.pre.PCV","Stockholm.pre.PCV") ~ as.integer(carriage_samples*100),
+                      TRUE ~ carriage_samples
+                    )
+                  ) %>%
+    dplyr::group_by(type) %>%
+    dplyr::mutate(strain_count = n_distinct(strain)) %>%
+    dplyr::ungroup() %>%
+    dplyr::group_by(strain) %>%
+    dplyr::mutate(type_count = n_distinct(type)) %>%
+    dplyr::ungroup() %>%
+    dplyr::filter(strain_count >= threshold_count | type_count >= threshold_count)
+
+sensitivity_S_pneumoniae_infant_strain %<>%
+    dplyr::mutate(study = factor(study, levels = studies_by_size[studies_by_size %in% unique(sensitivity_S_pneumoniae_infant_strain$study)]))
+
+sensitivity_S_pneumoniae_infant_strain %<>%
+    dplyr::mutate(type = factor(type,
+                                          levels = serotype_by_count[serotype_by_count %in% unique(sensitivity_S_pneumoniae_infant_strain$type)])) %>%
+  dplyr::mutate(strain = factor(strain))
+
+# Generate input for serotype models
+sensitivity_infant_serotype_invasiveness <- 
+  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
+                                            condense = FALSE)
+
+# Generate input for strain models
+sensitivity_infant_strain_invasiveness <- 
+  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
+                                            type = "strain",
+                                            condense = FALSE)
+
+# Generate input for strain and serotype models
+sensitivity_infant_serotype_and_strain_invasiveness <- 
+  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
+                                            use_strain = TRUE,
+                                            condense = FALSE)
+
+# Generate input for serotype models
+sensitivity_infant_serotype_strain_combined_invasiveness <- 
+  progressionEstimation::process_input_data(sensitivity_S_pneumoniae_infant_strain,
+                                            combine_strain = TRUE,
+                                            condense = FALSE)
+

Fit the first model:

+
sensitivity_adjusted_serotype_specific_poisson_fit <- 
+  progressionEstimation::fit_progression_rate_model(sensitivity_infant_serotype_invasiveness,
+                                                    type_specific = TRUE,
+                                                    location_adjustment = TRUE,
+                                                    stat_model = "poisson",
+                                                    model_description = "serotype_specific_poisson",
+                                                    num_chains = n_chains,
+                                                    num_iter = n_iter,
+                                                    num_cores = n_core,
+                                                    adapt_delta_value = adapt_delta,
+                                                    stepsize_value = stepsize,
+                                                    max_treedepth_value = max_treedepth)
+
+sensitivity_adjusted_serotype_specific_poisson_output_df <-
+  progressionEstimation::process_progression_rate_model_output(sensitivity_adjusted_serotype_specific_poisson_fit,
+                                                               sensitivity_S_pneumoniae_infant_strain,
+                                                               condense = FALSE)
+

+sensitivity_fit_list <- list(
+  sensitivity_adjusted_serotype_specific_poisson_fit,
+  sensitivity_adjusted_serotype_specific_negbin_fit,
+  sensitivity_adjusted_strain_specific_poisson_fit,
+  sensitivity_adjusted_strain_specific_negbin_fit,
+  sensitivity_adjusted_serotype_specific_strain_modified_poisson_fit,
+  sensitivity_adjusted_strain_specific_strain_modified_negbin_fit,
+  sensitivity_adjusted_strain_specific_serotype_modified_poisson_fit,
+  sensitivity_adjusted_strain_specific_serotype_modified_negbin_fit,
+  sensitivity_adjusted_strain_and_serotype_specific_poisson_fit,
+  sensitivity_adjusted_strain_and_serotype_specific_negbin_fit
+)
+
+sensitivity_bf_comparison <- 
+  progressionEstimation::compare_model_fits_with_bf(
+                                                    sensitivity_fit_list,
+                                                    num_iter = n_iter,
+                                                    num_threads = n_core)
+
+sensitivity_bf_comparison %>%
+  kableExtra::kable()  %>%
+  kableExtra::kable_styling(latex_options = "scale_down")
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Model + +log_Bayes_factor +
+serotype_specific_strain_modified_poisson + +0.000000 +
+serotype_specific_negbin + +-5.627929 +
+serotype_specific_strain_modified_negbin + +-5.940804 +
+serotype_specific_poisson + +-24.704099 +
+strain_specific_serotype_modified_poisson + +-25.281506 +
+strain_specific_serotype_modified_negbin + +-29.671881 +
+strain_and_serotype_specific_poisson + +-32.859631 +
+strain_specific_negbin + +-33.488613 +
+strain_and_serotype_specific_negbin + +-36.481845 +
+strain_specific_poisson --392.84378 +-49.395688
+

+write.csv(bf_comparison,
+          file = "child_strain_bf_sensitivity_comparison.csv",
+          quote = FALSE,
+          row.names = FALSE)
diff --git a/examples/serotype_phi_plot.pdf b/examples/serotype_phi_plot.pdf new file mode 100644 index 0000000..fe210e3 Binary files /dev/null and b/examples/serotype_phi_plot.pdf differ diff --git a/examples/serotype_phi_plot.png b/examples/serotype_phi_plot.png new file mode 100644 index 0000000..600c405 Binary files /dev/null and b/examples/serotype_phi_plot.png differ diff --git a/examples/serotype_rmse_plot.pdf b/examples/serotype_rmse_plot.pdf new file mode 100644 index 0000000..20abf59 Binary files /dev/null and b/examples/serotype_rmse_plot.pdf differ diff --git a/examples/serotype_rmse_plot.png b/examples/serotype_rmse_plot.png new file mode 100644 index 0000000..fed96ce Binary files /dev/null and b/examples/serotype_rmse_plot.png differ diff --git a/examples/strain_and_serotype_precision_plot.png b/examples/strain_and_serotype_precision_plot.png new file mode 100644 index 0000000..b3dc0a8 Binary files /dev/null and b/examples/strain_and_serotype_precision_plot.png differ diff --git a/examples/strain_and_serotype_rhat_plots.png b/examples/strain_and_serotype_rhat_plots.png new file mode 100644 index 0000000..33100c7 Binary files /dev/null and b/examples/strain_and_serotype_rhat_plots.png differ diff --git a/examples/strain_and_serotype_rmse_plot.png b/examples/strain_and_serotype_rmse_plot.png new file mode 100644 index 0000000..4f01f39 Binary files /dev/null and b/examples/strain_and_serotype_rmse_plot.png differ diff --git a/examples/strain_and_serotype_trace_plots.png b/examples/strain_and_serotype_trace_plots.png new file mode 100644 index 0000000..3c5220d Binary files /dev/null and b/examples/strain_and_serotype_trace_plots.png differ diff --git a/examples/study_adjusted_type_specific_negbin_serotype_fit.csv b/examples/study_adjusted_type_specific_negbin_serotype_fit.csv new file mode 100644 index 0000000..44560f2 --- /dev/null +++ b/examples/study_adjusted_type_specific_negbin_serotype_fit.csv @@ -0,0 +1,539 @@ +study,type,carriage_samples,surveillance_population,time_interval,carriage,disease,model_name,rho,rho_lower,rho_upper,delta,delta_lower,delta_upper,nu,nu_lower,nu_upper,phi,phi_lower,phi_upper,carriage_prediction,carriage_prediction_lower,carriage_prediction_upper,disease_prediction,disease_prediction_lower,disease_prediction_upper,carriage_rmse,disease_rmse,classification +Alabama.pre.PCV,1,827,19316,3.4,5,4,adjusted_type_specific_negbin,0.00546763867835361,0.0022296905142799,0.0114067123632732,1.32902312226788,0.639728473315217,2.7866382644382,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,4.52173718699844,1.84395405530948,9.43335112442689,8.12029131289895,2.98913828338317,22.146851879084,0.478262813001563,4.12029131289895,PCV10 +Alabama.pre.PCV,13,827,19316,3.4,6,0,adjusted_type_specific_negbin,0.00752105058861741,0.00314316072976064,0.0147535043335538,1.32902312226788,0.639728473315217,2.7866382644382,0.000641136431718939,0.000181165818687303,0.00210187050439682,3.54240797176599,2.49560124043154,5.15073328448319,6.2199088367866,2.59939392351205,12.201148083849,0.414220034160549,0.0902124315984192,1.62343474528297,0.219908836786601,0.414220034160549,No PCV +Alabama.pre.PCV,14,827,19316,3.4,20,18,adjusted_type_specific_negbin,0.0274602879659851,0.0181966730155034,0.0396516791035819,1.32902312226788,0.639728473315217,2.7866382644382,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,22.7096581478697,15.0486485838213,32.7919386186622,10.0445036506143,5.13355306881399,20.590847404438,2.70965814786968,7.95549634938573,PCV7 +Alabama.pre.PCV,20,827,19316,3.4,3,0,adjusted_type_specific_negbin,0.00407270898462721,0.00117138717793945,0.00991799632943284,1.32902312226788,0.639728473315217,2.7866382644382,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,3.3681303302867,0.968737196155926,8.20218296444096,0.266081256245148,0.0453396215235235,1.23213987376812,0.368130330286699,0.266081256245148,PPV23 +Alabama.pre.PCV,3,827,19316,3.4,35,0,adjusted_type_specific_negbin,0.0403859152039852,0.0281908722851858,0.0554781509907888,1.32902312226788,0.639728473315217,2.7866382644382,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,33.3991518736958,23.3138513798487,45.8804308693824,7.14182033818568,3.16601906397296,16.2943688525172,1.60084812630423,7.14182033818568,PCV13 +Alabama.pre.PCV,31,827,19316,3.4,0,1,adjusted_type_specific_negbin,0.00188504818351722,0.000271350360204483,0.00631793586569089,1.32902312226788,0.639728473315217,2.7866382644382,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,1.55893484776874,0.224406747889107,5.22493296092637,0.0772782879332689,0.00880749899395876,0.405232560253619,1.55893484776874,0.922721712066731,No PCV +Alabama.pre.PCV,37,827,19316,3.4,13,0,adjusted_type_specific_negbin,0.0163280657081594,0.00908738922642831,0.0264001217181338,1.32902312226788,0.639728473315217,2.7866382644382,8.73857936299313e-05,4.08275642783979e-06,0.000582177503837751,3.54240797176599,2.49560124043154,5.15073328448319,13.5033103406478,7.51527089025621,21.8329006608966,0.121140587267582,0.00549456383039424,0.880559377899026,0.503310340647817,0.121140587267582,No PCV +Alabama.pre.PCV,38,827,19316,3.4,3,0,adjusted_type_specific_negbin,0.00404710201019653,0.0011958052461254,0.00985996271386355,1.32902312226788,0.639728473315217,2.7866382644382,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,3.34695336243253,0.988930938545709,8.15418916436516,0.305267429912078,0.066042986680334,1.10899751534913,0.346953362432528,0.305267429912078,No PCV +Alabama.pre.PCV,4,827,19316,3.4,14,8,adjusted_type_specific_negbin,0.0205045098482851,0.0125301658442399,0.0313336038953097,1.32902312226788,0.639728473315217,2.7866382644382,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,16.9572296445318,10.3624471531864,25.9128904214211,3.4200091263624,1.54034909831241,7.48876017377047,2.95722964453175,4.5799908736376,PCV7 +Alabama.pre.PCV,5,827,19316,3.4,0,1,adjusted_type_specific_negbin,0.00111853386257082,0.000150157125535891,0.00418213251230768,1.32902312226788,0.639728473315217,2.7866382644382,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,0.925027504346072,0.124179942818182,3.45862358767845,0.708902074102332,0.0916621766717918,3.07366514578563,0.925027504346072,0.291097925897668,PCV10 +Alabama.pre.PCV,8,827,19316,3.4,4,0,adjusted_type_specific_negbin,0.0048094947098376,0.00165320713211589,0.0108391917581863,1.32902312226788,0.639728473315217,2.7866382644382,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,3.97745212503569,1.36720229825984,8.96401158402008,0.792078798224813,0.212142782389608,2.61118849523177,0.0225478749643075,0.792078798224813,PCV20 +Barcelona.post.PCV7,1,209,228000,4,2,39,adjusted_type_specific_negbin,0.015148709441001,0.00638320995784385,0.032498756714754,0.153863816016636,0.0938708758283483,0.254083449431664,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,3.16608027316921,1.33409088118937,6.79224015338358,36.3535806193399,16.5874238849298,83.6594469891157,1.16608027316921,2.64641938066006,PCV10 +Barcelona.post.PCV7,10A,209,228000,4,10,2,adjusted_type_specific_negbin,0.0457281860941858,0.0240492293567497,0.0782051336935313,0.153863816016636,0.0938708758283483,0.254083449431664,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,9.55719089368484,5.02628893556069,16.3448729419481,4.60439229997592,2.07200554418249,10.0404373065734,0.44280910631516,2.60439229997592,PCV20 +Barcelona.post.PCV7,11A,209,228000,4,9,0,adjusted_type_specific_negbin,0.0442601672930207,0.0221793895910638,0.0770916445731005,0.153863816016636,0.0938708758283483,0.254083449431664,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,9.25037496424133,4.63549242453233,16.112153715778,0.41631457791526,0.151141902656473,1.03064768004966,0.250374964241333,0.41631457791526,PCV20 +Barcelona.post.PCV7,14,209,228000,4,4,6,adjusted_type_specific_negbin,0.0175906651917694,0.00713294123272836,0.0383731430192383,0.153863816016636,0.0938708758283483,0.254083449431664,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,3.67644902507981,1.49078471764023,8.0199868910208,10.3991884821053,4.14248600054515,25.237773243558,0.323550974920194,4.39918848210534,PCV7 +Barcelona.post.PCV7,15A,209,228000,4,6,2,adjusted_type_specific_negbin,0.0321060978644995,0.0148633755985753,0.0598824521489811,0.153863816016636,0.0938708758283483,0.254083449431664,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,6.71017445368039,3.10644550010224,12.515432499137,1.86322684139056,0.72650998813631,4.46693546110601,0.710174453680395,0.136773158609438,No PCV +Barcelona.post.PCV7,15B/C,209,228000,4,13,3,adjusted_type_specific_negbin,0.0648128434880877,0.0375767443047139,0.101103649410229,0.153863816016636,0.0938708758283483,0.254083449431664,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,13.5458842890103,7.8535395596852,21.1306627267378,3.15878763900267,1.53486396053582,6.27211660507352,0.545884289010331,0.158787639002668,PCV20 +Barcelona.post.PCV7,16F,209,228000,4,5,2,adjusted_type_specific_negbin,0.0283265281920388,0.0125834147774669,0.0544543398296637,0.153863816016636,0.0938708758283483,0.254083449431664,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,5.92024439213612,2.62993368849059,11.3809570243997,1.56344059209953,0.57200231927615,3.94154603405911,0.920244392136117,0.436559407900466,No PCV +Barcelona.post.PCV7,17F,209,228000,4,5,0,adjusted_type_specific_negbin,0.0226805466315472,0.00861209597380072,0.0474327078121079,0.153863816016636,0.0938708758283483,0.254083449431664,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,4.74023424599337,1.79992805852435,9.91343593273055,1.21359566493502,0.373533072055718,3.35931139592153,0.25976575400663,1.21359566493502,PPV23 +Barcelona.post.PCV7,19A,209,228000,4,21,34,adjusted_type_specific_negbin,0.109394106245757,0.0738338292746688,0.154051398284424,0.153863816016636,0.0938708758283483,0.254083449431664,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,22.8633682053633,15.4312703184058,32.1967422414445,23.671436878242,13.8920709470333,41.0550467713373,1.86336820536331,10.328563121758,PCV13 +Barcelona.post.PCV7,19F,209,228000,4,13,7,adjusted_type_specific_negbin,0.0666493546630558,0.0395961795900188,0.104011016544191,0.153863816016636,0.0938708758283483,0.254083449431664,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,13.9297151245787,8.27560153431393,21.7383024577359,6.01469096719291,3.11099707060422,11.4781613150903,0.929715124578657,0.985309032807093,PCV7 +Barcelona.post.PCV7,21,209,228000,4,5,0,adjusted_type_specific_negbin,0.0241282435166282,0.00931324621128912,0.0500562720019193,0.153863816016636,0.0938708758283483,0.254083449431664,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,5.04280289497529,1.94646845815943,10.4617608484011,0.670622222946079,0.19483751699974,1.94736416353175,0.0428028949752921,0.670622222946079,No PCV +Barcelona.post.PCV7,22F,209,228000,4,8,3,adjusted_type_specific_negbin,0.0370594277991248,0.0184415323283995,0.0656292773613424,0.153863816016636,0.0938708758283483,0.254083449431664,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,7.74542041001708,3.85428025663549,13.7165189685206,5.3360078844169,2.29858051543166,11.9028504577637,0.254579589982919,2.3360078844169,PCV15 +Barcelona.post.PCV7,23A,209,228000,4,9,0,adjusted_type_specific_negbin,0.0424632751199378,0.0210860878489547,0.0745045251368515,0.153863816016636,0.0938708758283483,0.254083449431664,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,8.87482450006699,4.40699236043153,15.571445753602,0.944928951353759,0.366607607916578,2.22407845209074,0.125175499933007,0.944928951353759,No PCV +Barcelona.post.PCV7,23B,209,228000,4,17,5,adjusted_type_specific_negbin,0.0881905788594055,0.0566172201548735,0.129424886558139,0.153863816016636,0.0938708758283483,0.254083449431664,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,18.4318309816158,11.8329990123686,27.049801290651,3.18800762897513,1.55310161395033,6.47997072588612,1.43183098161575,1.81199237102487,No PCV +Barcelona.post.PCV7,23F,209,228000,4,7,4,adjusted_type_specific_negbin,0.0375957398760549,0.0188184851515382,0.0662397453075905,0.153863816016636,0.0938708758283483,0.254083449431664,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,7.85750963409547,3.93306339667148,13.8441067692864,3.62219417677654,1.661766257006,7.60226125965463,0.857509634095472,0.377805823223458,PCV7 +Barcelona.post.PCV7,3,209,228000,4,2,8,adjusted_type_specific_negbin,0.0185513160444266,0.00791524037125946,0.0376278857726665,0.153863816016636,0.0938708758283483,0.254083449431664,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,3.87722505328515,1.65428523759323,7.86422812648729,5.25661414670543,2.26734090233956,11.604905947399,1.87722505328515,2.74338585329457,PCV13 +Barcelona.post.PCV7,34,209,228000,4,6,0,adjusted_type_specific_negbin,0.0298925884783963,0.0126260836699104,0.0578879624239336,0.153863816016636,0.0938708758283483,0.254083449431664,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,6.24755099198482,2.63885148701128,12.0985841466021,0.408843302000972,0.0754201069822134,1.57081321151485,0.24755099198482,0.408843302000972,No PCV +Barcelona.post.PCV7,35B,209,228000,4,5,0,adjusted_type_specific_negbin,0.0249778790824747,0.00985711658099527,0.0512837685722245,0.153863816016636,0.0938708758283483,0.254083449431664,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,5.22037672823722,2.06013736542801,10.7183076315949,0.450923018476005,0.132310113147227,1.31701492308051,0.220376728237218,0.450923018476005,No PCV +Barcelona.post.PCV7,5,209,228000,4,0,14,adjusted_type_specific_negbin,0.00972214571874939,0.00332132957847883,0.023944918213947,0.153863816016636,0.0938708758283483,0.254083449431664,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,2.03192845521862,0.694157881902076,5.00448790671492,9.74787142922688,4.04495966197693,24.7985909919992,2.03192845521862,4.25212857077312,PCV10 +Barcelona.post.PCV7,6A,209,228000,4,16,4,adjusted_type_specific_negbin,0.0780291816254323,0.0479996511601518,0.118179577288974,0.153863816016636,0.0938708758283483,0.254083449431664,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,16.3080989597153,10.0319270924717,24.6995316533956,4.7486757853963,2.3924178271899,9.13841714740917,0.308098959715345,0.748675785396303,PCV13 +Barcelona.post.PCV7,6B,209,228000,4,4,2,adjusted_type_specific_negbin,0.0217497819833855,0.0088278548717226,0.044104367151299,0.153863816016636,0.0938708758283483,0.254083449431664,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,4.54570443452758,1.84502166819002,9.2178127346215,2.26995918103694,0.860471819762928,5.29509914510442,0.545704434527578,0.269959181036936,PCV7 +Barcelona.post.PCV7,6C,209,228000,4,19,1,adjusted_type_specific_negbin,0.0931012630824605,0.0596946011924903,0.136464732674915,0.153863816016636,0.0938708758283483,0.254083449431664,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,19.4581639842342,12.4761716492305,28.5211291290572,1.08438827799772,0.410056188039555,2.71895095212823,0.458163984234233,0.0843882779977212,No PCV +Barcelona.post.PCV7,7F,209,228000,4,0,14,adjusted_type_specific_negbin,0.00816635039448159,0.0029710049712753,0.0202767714455849,0.153863816016636,0.0938708758283483,0.254083449431664,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,1.70676723244665,0.620940038996537,4.23784523212724,10.8458032675299,4.38511144773494,27.1009869664935,1.70676723244665,3.15419673247014,PCV10 +Bogota.post.PCV7,1,246,357200,1,0,8,adjusted_type_specific_negbin,0.00238978074392515,0.000658874562650796,0.00827251357460694,0.659326180327527,0.383560910417084,1.12788434024843,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,0.587886063005586,0.162083142412096,2.03503833935331,9.59238221238897,3.06454864758885,32.2573929580101,0.587886063005586,1.59238221238897,PCV10 +Bogota.post.PCV7,10A,246,357200,1,1,0,adjusted_type_specific_negbin,0.00432123657239775,0.000597528683573622,0.0157307457112238,0.659326180327527,0.383560910417084,1.12788434024843,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,1.06302419680985,0.146992056159111,3.86976344496107,0.731240569382864,0.0992638522862014,2.88730489655631,0.0630241968098475,0.731240569382864,PCV20 +Bogota.post.PCV7,11A,246,357200,1,7,2,adjusted_type_specific_negbin,0.0356629102663337,0.0177267932191576,0.0629396184850307,0.659326180327527,0.383560910417084,1.12788434024843,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,8.77307592551808,4.36079113191278,15.4831461473176,0.561190659156622,0.203475515162186,1.40188209370146,1.77307592551808,1.43880934084338,PCV20 +Bogota.post.PCV7,13,246,357200,1,1,0,adjusted_type_specific_negbin,0.00444581583538823,0.000593856990048783,0.016302846530519,0.659326180327527,0.383560910417084,1.12788434024843,0.000641136431718939,0.000181165818687303,0.00210187050439682,3.54240797176599,2.49560124043154,5.15073328448319,1.09367069550551,0.146088819552001,4.01050024650767,0.654789262458424,0.0790655392294931,3.20812164236197,0.0936706955055053,0.654789262458424,No PCV +Bogota.post.PCV7,14,246,357200,1,3,14,adjusted_type_specific_negbin,0.0150401364549343,0.00641694573512272,0.0314485122752235,0.659326180327527,0.383560910417084,1.12788434024843,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,3.69987356791385,1.57856865084019,7.73633401970499,14.8243976114033,6.43571641625122,33.8482625507256,0.699873567913845,0.824397611403285,PCV7 +Bogota.post.PCV7,15A,246,357200,1,2,2,adjusted_type_specific_negbin,0.0130244228263078,0.0042692343969376,0.0302336363765965,0.659326180327527,0.383560910417084,1.12788434024843,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,3.20400801527173,1.05023166164665,7.43747454864273,1.2591420014277,0.383970200873982,3.50282670010356,1.20400801527173,0.740857998572298,No PCV +Bogota.post.PCV7,15B/C,246,357200,1,13,5,adjusted_type_specific_negbin,0.0560405699485901,0.0331987502501277,0.0876812811443389,0.659326180327527,0.383560910417084,1.12788434024843,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,13.7859802073532,8.16689256153142,21.5695951615074,4.58776590918012,2.25446493099824,9.25525876101771,0.785980207353175,0.412234090819876,PCV20 +Bogota.post.PCV7,16F,246,357200,1,1,2,adjusted_type_specific_negbin,0.0101001463249339,0.00285449359089892,0.0254654222357431,0.659326180327527,0.383560910417084,1.12788434024843,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,2.48463599593373,0.702205423361134,6.2644938699928,0.936793859444906,0.241418206694389,2.77357232959948,1.48463599593373,1.06320614055509,No PCV +Bogota.post.PCV7,17F,246,357200,1,2,0,adjusted_type_specific_negbin,0.00831834563187431,0.00193083737532205,0.0232618386721024,0.659326180327527,0.383560910417084,1.12788434024843,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,2.04631302544108,0.474985994329225,5.72241231333718,0.743618042739592,0.153457179495874,2.56532113319903,0.0463130254410817,0.743618042739592,PPV23 +Bogota.post.PCV7,18A,246,357200,1,1,0,adjusted_type_specific_negbin,0.00559087668174825,0.000784502255197723,0.01945601256444,0.659326180327527,0.383560910417084,1.12788434024843,0.000198001510080884,2.43125238691192e-05,0.000991711750205049,3.54240797176599,2.49560124043154,5.15073328448319,1.37535566371007,0.19298755477864,4.78617909085225,0.243965785138043,0.0177559603450845,1.68536727478812,0.37535566371007,0.243965785138043,No PCV +Bogota.post.PCV7,18C,246,357200,1,2,5,adjusted_type_specific_negbin,0.00970197804379122,0.00333353964429133,0.0236000224426641,0.659326180327527,0.383560910417084,1.12788434024843,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,2.38668659877264,0.820050752495668,5.80560552089537,6.14018068954665,2.14751029394348,16.6019296464353,0.38668659877264,1.14018068954665,PCV7 +Bogota.post.PCV7,19A,246,357200,1,3,5,adjusted_type_specific_negbin,0.0147757711874532,0.00590154323167141,0.0317498784828028,0.659326180327527,0.383560910417084,1.12788434024843,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,3.63483971211348,1.45177963499117,7.81047010676948,5.36048604760553,2.09945046030501,12.6410997112201,0.634839712113479,0.360486047605532,PCV13 +Bogota.post.PCV7,19B,246,357200,1,1,0,adjusted_type_specific_negbin,0.00648162923254371,0.000886801619109344,0.0216767400886542,0.659326180327527,0.383560910417084,1.12788434024843,1.22017298254343e-05,1.14070066130824e-06,0.000456117500379924,3.54240797176599,2.49560124043154,5.15073328448319,1.59448079120575,0.218153198300899,5.33247806180893,0.0179927634127981,0.000713873744293639,0.684995730178288,0.594480791205752,0.0179927634127981,No PCV +Bogota.post.PCV7,19F,246,357200,1,3,2,adjusted_type_specific_negbin,0.0144859222118954,0.00523676732939474,0.0324102197778823,0.659326180327527,0.383560910417084,1.12788434024843,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,3.56353686412627,1.28824476303111,7.97291406535905,2.18921197147313,0.754050027967658,5.57360366107144,0.563536864126272,0.189211971473125,PCV7 +Bogota.post.PCV7,20,246,357200,1,0,1,adjusted_type_specific_negbin,0.00377820684900715,0.000460450408149297,0.0146702646115612,0.659326180327527,0.383560910417084,1.12788434024843,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,0.929438884855758,0.113270800404727,3.60888509444407,0.662442772098279,0.0775329284534279,3.15109045666868,0.929438884855758,0.337557227901721,PPV23 +Bogota.post.PCV7,22F,246,357200,1,0,1,adjusted_type_specific_negbin,0.00345954221631657,0.000464705750888089,0.0128133202684218,0.659326180327527,0.383560910417084,1.12788434024843,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,0.851047385213876,0.11431761471847,3.15207678603177,0.835798435158679,0.111302882356698,3.25015098872159,0.851047385213876,0.164201564841321,PCV15 +Bogota.post.PCV7,23A,246,357200,1,6,0,adjusted_type_specific_negbin,0.0240192592307942,0.0101049889842797,0.0473780278675782,0.659326180327527,0.383560910417084,1.12788434024843,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,5.90873777077537,2.48582729013282,11.6549948554242,0.898018866384006,0.304515964680818,2.33703263038252,0.0912622292246343,0.898018866384006,No PCV +Bogota.post.PCV7,23B,246,357200,1,1,1,adjusted_type_specific_negbin,0.00848623398677966,0.00196263366507608,0.0234453208888689,0.659326180327527,0.383560910417084,1.12788434024843,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,2.0876135607478,0.482807881608715,5.76754893866176,0.513809668578068,0.104646746381237,1.67877532957672,1.0876135607478,0.486190331421932,No PCV +Bogota.post.PCV7,23F,246,357200,1,5,4,adjusted_type_specific_negbin,0.0234784923924964,0.0107444459451767,0.0450154848860625,0.659326180327527,0.383560910417084,1.12788434024843,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,5.77570912855412,2.64313370251346,11.0738092819714,3.80484526509228,1.6106678864196,8.39851923411978,0.77570912855412,0.195154734907718,PCV7 +Bogota.post.PCV7,24F,246,357200,1,1,1,adjusted_type_specific_negbin,0.00420113425063384,0.000800295130474419,0.0143946412492578,0.659326180327527,0.383560910417084,1.12788434024843,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,1.03347902565593,0.196872602096707,3.54108174731741,2.16003705394989,0.422941339405152,7.93673987552462,0.0334790256559256,1.16003705394989,No PCV +Bogota.post.PCV7,25A,246,357200,1,0,3,adjusted_type_specific_negbin,0.00537602993327753,0.00118738575015112,0.0165213130213356,0.659326180327527,0.383560910417084,1.12788434024843,0.00165141051651395,0.000589976401575755,0.00500660807717493,3.54240797176599,2.49560124043154,5.15073328448319,1.32250336358627,0.292096894537174,4.06424300324855,2.06158904108501,0.50908687427637,6.8480059024469,1.32250336358627,0.93841095891499,No PCV +Bogota.post.PCV7,28A,246,357200,1,0,2,adjusted_type_specific_negbin,0.00280272750065095,9.87715951111349e-05,0.0149886570811495,0.659326180327527,0.383560910417084,1.12788434024843,0.00301090213061906,0.000175700001064865,0.122447055697762,3.54240797176599,2.49560124043154,5.15073328448319,0.689470965160133,0.0242978123973392,3.68720964196277,1.85537007061426,0.227000552063607,11.3611231399606,0.689470965160133,0.144629929385744,No PCV +Bogota.post.PCV7,29,246,357200,1,1,0,adjusted_type_specific_negbin,0.00624059540546693,0.000875761333844071,0.020836840477833,0.659326180327527,0.383560910417084,1.12788434024843,6.39161619681567e-05,3.15448575829138e-06,0.000496397918354293,3.54240797176599,2.49560124043154,5.15073328448319,1.53518646974486,0.215437288125641,5.12586275754691,0.0860199258031082,0.00316625396996435,0.87990430701699,0.535186469744864,0.0860199258031082,No PCV +Bogota.post.PCV7,3,246,357200,1,1,12,adjusted_type_specific_negbin,0.0144637162563364,0.00629661836907218,0.0299437333625467,0.659326180327527,0.383560910417084,1.12788434024843,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,3.55807419905876,1.54896811879176,7.36615840718648,6.86984222558877,3.11560766283729,15.0690271827381,2.55807419905876,5.13015777441123,PCV13 +Bogota.post.PCV7,35B,246,357200,1,5,2,adjusted_type_specific_negbin,0.0266616457491089,0.0117858917522195,0.0503545814154764,0.659326180327527,0.383560910417084,1.12788434024843,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,6.55876485428078,2.89932937104599,12.3872270282072,0.805898220452978,0.269166894334623,2.16069946279568,1.55876485428078,1.19410177954702,No PCV +Bogota.post.PCV7,35F,246,357200,1,3,0,adjusted_type_specific_negbin,0.0132016461804501,0.00396755151243216,0.0316190164290536,0.659326180327527,0.383560910417084,1.12788434024843,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,3.24760496039073,0.97601767205831,7.77827804154719,0.457947362502907,0.109766006903214,1.47370870058143,0.247604960390733,0.457947362502907,No PCV +Bogota.post.PCV7,4,246,357200,1,0,1,adjusted_type_specific_negbin,0.00257502711686429,0.000317733534185445,0.0102732120945686,0.659326180327527,0.383560910417084,1.12788434024843,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,0.633456670748616,0.0781624494096195,2.52721017526388,1.15845076387285,0.146691809492726,4.79150047481713,0.633456670748616,0.158450763872852,PCV7 +Bogota.post.PCV7,42,246,357200,1,1,0,adjusted_type_specific_negbin,0.00636966040218624,0.000905717515335018,0.021370655858204,0.659326180327527,0.383560910417084,1.12788434024843,1.64727034476203e-05,1.1485247591461e-06,0.000721087752303597,3.54240797176599,2.49560124043154,5.15073328448319,1.56693645893781,0.222806508772414,5.25718134111817,0.0243497779891329,0.00079819550507225,0.985304163600511,0.566936458937815,0.0243497779891329,No PCV +Bogota.post.PCV7,5,246,357200,1,0,1,adjusted_type_specific_negbin,0.00107393168874131,0.000113261688132647,0.00576710095679433,0.659326180327527,0.383560910417084,1.12788434024843,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,0.264187195430362,0.0278623752806312,1.4187068353714,1.84670428350929,0.227342965856133,9.44751749182545,0.264187195430362,0.846704283509288,PCV10 +Bogota.post.PCV7,6A,246,357200,1,6,1,adjusted_type_specific_negbin,0.0238288913936225,0.0102824243178266,0.0461770250163375,0.659326180327527,0.383560910417084,1.12788434024843,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,5.86190728283114,2.52947638218534,11.359548154019,2.41643028292432,0.935513324195321,5.71929369135309,0.138092717168862,1.41643028292432,PCV13 +Bogota.post.PCV7,6B,246,357200,1,2,4,adjusted_type_specific_negbin,0.0144629982379777,0.00555179619303538,0.031011987477623,0.659326180327527,0.383560910417084,1.12788434024843,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,3.55789756654252,1.3657418634867,7.62894891949525,2.53071654981648,0.940157341616856,6.04261440891715,1.55789756654252,1.46928345018352,PCV7 +Bogota.post.PCV7,6C,246,357200,1,2,0,adjusted_type_specific_negbin,0.00997115753756139,0.00222445003151163,0.0271427985586209,0.659326180327527,0.383560910417084,1.12788434024843,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,2.4529047542401,0.547214707751861,6.67712844542074,0.192523222229938,0.0347986780604893,0.72308888984875,0.452904754240102,0.192523222229938,No PCV +Bogota.post.PCV7,7C,246,357200,1,1,0,adjusted_type_specific_negbin,0.00508434213536669,0.000692475094639737,0.018002174792152,0.659326180327527,0.383560910417084,1.12788434024843,0.000395968078807268,0.000112206548547661,0.00124464123083086,3.54240797176599,2.49560124043154,5.15073328448319,1.25074816530021,0.170348873281375,4.4285349988694,0.452755372469921,0.0534455426743512,2.23960916678535,0.250748165300207,0.452755372469921,No PCV +Bogota.post.PCV7,8,246,357200,1,0,2,adjusted_type_specific_negbin,0.00383122112246097,0.000754418784412701,0.0129875757527925,0.659326180327527,0.383560910417084,1.12788434024843,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,0.942480396125399,0.185587020965525,3.19494363518695,1.71256144982793,0.354595876674148,6.09918461435635,0.942480396125399,0.287438550172069,PCV20 +Bogota.post.PCV7,9V,246,357200,1,0,2,adjusted_type_specific_negbin,0.00369354411096549,0.000723988317554256,0.0125487194124628,0.659326180327527,0.383560910417084,1.12788434024843,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,0.908611851297512,0.178101126118347,3.08698497546586,1.78232704098034,0.362282706235538,6.19220390235521,0.908611851297512,0.21767295901966,PCV7 +Bogota.pre.PCV,1,197,357200,4,0,29,adjusted_type_specific_negbin,0.00518940946006615,0.00179759991976584,0.0147055660012012,0.233250072846497,0.144992589116746,0.379897747934858,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,1.02231366363303,0.354127184193871,2.89699650223664,29.5022377941163,11.9303919923364,81.992869560149,1.02231366363303,0.50223779411629,PCV10 +Bogota.pre.PCV,10A,197,357200,4,3,1,adjusted_type_specific_negbin,0.0132351698766249,0.00410742974645186,0.032251956529825,0.233250072846497,0.144992589116746,0.379897747934858,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,2.6073284656951,0.809163660051017,6.35363543637552,3.15906114746037,0.94169419038047,8.7317810233863,0.392671534304895,2.15906114746037,PCV20 +Bogota.pre.PCV,10B,197,357200,4,0,1,adjusted_type_specific_negbin,0.00439258975520387,0.000519726071929568,0.0175353137825186,0.233250072846497,0.144992589116746,0.379897747934858,0.000509389844494032,8.66360486448286e-05,0.00249463469166522,3.54240797176599,2.49560124043154,5.15073328448319,0.865340181775162,0.102386036170125,3.45445681515616,0.716560527959376,0.0736468856220443,3.8047926159483,0.865340181775162,0.283439472040624,No PCV +Bogota.pre.PCV,11A,197,357200,4,4,1,adjusted_type_specific_negbin,0.0252263577854627,0.0097156579209966,0.0521663437925191,0.233250072846497,0.144992589116746,0.379897747934858,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,4.96959248373615,1.91398461043633,10.2767697271263,0.560944851721254,0.176572932688306,1.51978788280499,0.969592483736151,0.439055148278746,PCV20 +Bogota.pre.PCV,12F,197,357200,4,0,3,adjusted_type_specific_negbin,0.00205251404103431,0.000389217315531362,0.00853155904696225,0.233250072846497,0.144992589116746,0.379897747934858,0.00604185287379925,0.00279991943562254,0.0141061491643519,3.54240797176599,2.49560124043154,5.15073328448319,0.404345266083759,0.0766758111596782,1.68071713225156,4.08964457661563,0.92220621213191,16.6278531238733,0.404345266083759,1.08964457661563,PCV20 +Bogota.pre.PCV,13,197,357200,4,1,4,adjusted_type_specific_negbin,0.0125110658564646,0.00379642196777262,0.0312906752697543,0.233250072846497,0.144992589116746,0.379897747934858,0.000641136431718939,0.000181165818687303,0.00210187050439682,3.54240797176599,2.49560124043154,5.15073328448319,2.46467997372353,0.747895127651205,6.16426302814159,2.5948671388554,0.747774772594835,8.20695078001524,1.46467997372353,1.4051328611446,No PCV +Bogota.pre.PCV,14,197,357200,4,9,163,adjusted_type_specific_negbin,0.0633334668869123,0.0387395364523858,0.097894599515503,0.233250072846497,0.144992589116746,0.379897747934858,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,12.4766929767217,7.63168868112001,19.2852361045541,88.8436900900059,52.1405278905687,155.790493923884,3.47669297672172,74.1563099099941,PCV7 +Bogota.pre.PCV,15A,197,357200,4,0,1,adjusted_type_specific_negbin,0.00485170216315162,0.000655219569699233,0.0177027751226357,0.233250072846497,0.144992589116746,0.379897747934858,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,0.95578532614087,0.129078255230749,3.48744669915923,0.673528548318509,0.0900288438657357,2.64570409678475,0.95578532614087,0.326471451681491,No PCV +Bogota.pre.PCV,15B/C,197,357200,4,6,2,adjusted_type_specific_negbin,0.0302425290317239,0.0134810021961938,0.0579968987567865,0.233250072846497,0.144992589116746,0.379897747934858,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,5.95777821924961,2.65575743265018,11.4253890550869,3.50431826021889,1.43901723582211,7.85495188871922,0.0422217807503928,1.50431826021889,PCV20 +Bogota.pre.PCV,15F,197,357200,4,1,0,adjusted_type_specific_negbin,0.00654335923277709,0.000922982601057751,0.0228163289587478,0.233250072846497,0.144992589116746,0.379897747934858,0.000170123300166289,2.02083655214776e-05,0.000864026455062348,3.54240797176599,2.49560124043154,5.15073328448319,1.28904176885709,0.181827572408377,4.49481680487332,0.345862372652258,0.0252482266729665,2.29379060809811,0.289041768857087,0.345862372652258,No PCV +Bogota.pre.PCV,16F,197,357200,4,1,3,adjusted_type_specific_negbin,0.0129728144468931,0.00413084024894219,0.0316284960280045,0.233250072846497,0.144992589116746,0.379897747934858,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,2.55564444603794,0.813775529041611,6.23081371751689,1.69421168712528,0.520746699239993,4.68259432153955,1.55564444603794,1.30578831287472,No PCV +Bogota.pre.PCV,18A,197,357200,4,1,1,adjusted_type_specific_negbin,0.00964515907602334,0.00204835740990742,0.0285143081032595,0.233250072846497,0.144992589116746,0.379897747934858,0.000198001510080884,2.43125238691192e-05,0.000991711750205049,3.54240797176599,2.49560124043154,5.15073328448319,1.9000963379766,0.403526409751761,5.61731869634213,0.607504398673948,0.0660766916366587,3.18316836893448,0.900096337976598,0.392495601326052,No PCV +Bogota.pre.PCV,18B,197,357200,4,0,1,adjusted_type_specific_negbin,0.00282267995215721,0.000301942896741279,0.0134784593532175,0.233250072846497,0.144992589116746,0.379897747934858,0.00124945709832586,0.000238400207766176,0.00647740004764962,3.54240797176599,2.49560124043154,5.15073328448319,0.55606795057497,0.059482750658032,2.65525649258385,1.14986624968605,0.136287198382841,5.90079468236472,0.55606795057497,0.149866249686053,No PCV +Bogota.pre.PCV,18C,197,357200,4,3,11,adjusted_type_specific_negbin,0.0160500872190239,0.00639137711975874,0.0357761173839256,0.233250072846497,0.144992589116746,0.379897747934858,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,3.16186718214772,1.25910129259247,7.04789512463335,14.4157632138074,5.8797691954441,36.2884539000688,0.161867182147716,3.41576321380741,PCV7 +Bogota.pre.PCV,18F,197,357200,4,0,2,adjusted_type_specific_negbin,0.00558435403000186,0.000723603831978427,0.021793571743035,0.233250072846497,0.144992589116746,0.379897747934858,0.000728671850027043,6.36008620504993e-05,0.00682715327525218,3.54240797176599,2.49560124043154,5.15073328448319,1.10011774391037,0.14254995489975,4.29333363337789,1.29596889849097,0.150594613589447,6.88878798201898,1.10011774391037,0.704031101509033,No PCV +Bogota.pre.PCV,19A,197,357200,4,3,10,adjusted_type_specific_negbin,0.019500858446192,0.00832618489739559,0.040581643271425,0.233250072846497,0.144992589116746,0.379897747934858,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,3.84166911389982,1.64025842478693,7.99458372447073,9.98806631670226,4.37138452346233,22.1688621991514,0.841669113899818,0.0119336832977446,PCV13 +Bogota.pre.PCV,19B,197,357200,4,1,0,adjusted_type_specific_negbin,0.0078974698363375,0.00111499608930923,0.0260718855333288,0.233250072846497,0.144992589116746,0.379897747934858,1.22017298254343e-05,1.14070066130824e-06,0.000456117500379924,3.54240797176599,2.49560124043154,5.15073328448319,1.55580155775849,0.219654229593918,5.13616145006577,0.0320754552871116,0.00139440240026344,1.06728154644551,0.555801557758488,0.0320754552871116,No PCV +Bogota.pre.PCV,19F,197,357200,4,25,13,adjusted_type_specific_negbin,0.122704725751578,0.08226452565429,0.17236593206673,0.233250072846497,0.144992589116746,0.379897747934858,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,24.1728309730609,16.2061115538951,33.9560886171458,26.2358973093435,14.3981696746403,47.9787837121667,0.827169026939103,13.2358973093435,PCV7 +Bogota.pre.PCV,22F,197,357200,4,0,2,adjusted_type_specific_negbin,0.00491105630861914,0.000983223207313575,0.0161866321358961,0.233250072846497,0.144992589116746,0.379897747934858,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,0.96747809279797,0.193694971840774,3.18876653077153,1.67633866613651,0.344332962464835,5.66137265307242,0.96747809279797,0.323661333863493,PCV15 +Bogota.pre.PCV,23A,197,357200,4,5,2,adjusted_type_specific_negbin,0.0301228601539838,0.0131715398431897,0.0576362274903537,0.233250072846497,0.144992589116746,0.379897747934858,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,5.9342034503348,2.59479334910836,11.3543368155997,1.58659509000897,0.593389551804199,3.82208893680498,0.934203450334799,0.413404909991028,No PCV +Bogota.pre.PCV,23B,197,357200,4,2,1,adjusted_type_specific_negbin,0.0131219688976195,0.00384562544081816,0.0323508398185267,0.233250072846497,0.144992589116746,0.379897747934858,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,2.58502787283105,0.757588211841178,6.37311544424976,1.12531341549786,0.30125028562262,3.25008552364356,0.585027872831046,0.125313415497862,No PCV +Bogota.pre.PCV,23F,197,357200,4,7,9,adjusted_type_specific_negbin,0.0391870177114623,0.0201500179639374,0.0687887987529075,0.233250072846497,0.144992589116746,0.379897747934858,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,7.71984248915808,3.96955353889566,13.5513933543228,8.96830689367292,4.30638911255577,18.2876180624638,0.719842489158076,0.0316931063270776,PCV7 +Bogota.pre.PCV,24F,197,357200,4,0,2,adjusted_type_specific_negbin,0.00317176561844652,0.000570652901532538,0.0119351377822606,0.233250072846497,0.144992589116746,0.379897747934858,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,0.624837826833965,0.11241862160191,2.35122214310534,2.30907226013404,0.453854976613308,8.72293231090822,0.624837826833965,0.309072260134043,No PCV +Bogota.pre.PCV,25A,197,357200,4,1,2,adjusted_type_specific_negbin,0.0059266242236317,0.00130254104044687,0.0192737215028864,0.233250072846497,0.144992589116746,0.379897747934858,0.00165141051651395,0.000589976401575755,0.00500660807717493,3.54240797176599,2.49560124043154,5.15073328448319,1.16754497205545,0.256600584968034,3.79692313606862,3.20948074356584,0.755381853829915,11.7946167321746,0.167544972055446,1.20948074356584,No PCV +Bogota.pre.PCV,3,197,357200,4,1,6,adjusted_type_specific_negbin,0.00915007073886288,0.00307481466799092,0.02341743957908,0.233250072846497,0.144992589116746,0.379897747934858,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,1.80256393555599,0.605738489594211,4.61323559707876,6.15622252708742,2.19416315345513,16.4136159125469,0.802563935555987,0.156222527087417,PCV13 +Bogota.pre.PCV,34,197,357200,4,3,0,adjusted_type_specific_negbin,0.0160012527847135,0.00466910486311523,0.0383285756321955,0.233250072846497,0.144992589116746,0.379897747934858,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,3.15224679858856,0.9198136580337,7.55072939954252,0.515318566559097,0.083015253445866,2.13858398397177,0.152246798588561,0.515318566559097,No PCV +Bogota.pre.PCV,35C,197,357200,4,0,1,adjusted_type_specific_negbin,0.00347181251893524,0.000123017094561154,0.0187263001671386,0.233250072846497,0.144992589116746,0.379897747934858,0.00068871049193812,1.47981860372811e-05,0.0345205695664563,3.54240797176599,2.49560124043154,5.15073328448319,0.683947066230243,0.0242343676285474,3.68908113292631,0.764600125987189,0.0260965418497661,6.58841329346583,0.683947066230243,0.235399874012811,No PCV +Bogota.pre.PCV,35F,197,357200,4,2,1,adjusted_type_specific_negbin,0.0144695349571462,0.0041964438268123,0.0355130155630023,0.233250072846497,0.144992589116746,0.379897747934858,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,2.85049838655781,0.826699433882023,6.99606406591144,0.714782409199541,0.177856576935268,2.20858988204569,0.85049838655781,0.285217590800459,No PCV +Bogota.pre.PCV,4,197,357200,4,2,5,adjusted_type_specific_negbin,0.0109942382905546,0.00372684685450457,0.0274374762459666,0.233250072846497,0.144992589116746,0.379897747934858,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,2.16586494323925,0.7341888303374,5.40518282045543,6.95793198401948,2.43513939041971,18.8165329749432,0.165864943239251,1.95793198401948,PCV7 +Bogota.pre.PCV,5,197,357200,4,0,5,adjusted_type_specific_negbin,0.00259462684748207,0.000571709489434563,0.0101333543678272,0.233250072846497,0.144992589116746,0.379897747934858,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,0.511141488953968,0.112626769418609,1.99627081046196,6.23880806797273,1.7603638663643,22.536864702821,0.511141488953968,1.23880806797273,PCV10 +Bogota.pre.PCV,6A,197,357200,4,23,16,adjusted_type_specific_negbin,0.118960949583657,0.0813593978963427,0.165794340873853,0.233250072846497,0.144992589116746,0.379897747934858,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,23.4353070679804,16.0278013855795,32.6614851521491,17.1529368320654,9.57424029925147,30.9501267407697,0.435307067980414,1.15293683206538,PCV13 +Bogota.pre.PCV,6B,197,357200,4,12,26,adjusted_type_specific_negbin,0.0711994044490136,0.0437364809778733,0.108241449775086,0.233250072846497,0.144992589116746,0.379897747934858,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,14.0262826764557,8.61608675264104,21.323565605692,17.6533515819258,9.83541326299015,32.2952457879567,2.02628267645567,8.34664841807416,PCV7 +Bogota.pre.PCV,7C,197,357200,4,0,1,adjusted_type_specific_negbin,0.00490481495256957,0.000641759523221264,0.0184536223503115,0.233250072846497,0.144992589116746,0.379897747934858,0.000395968078807268,0.000112206548547661,0.00124464123083086,3.54240797176599,2.49560124043154,5.15073328448319,0.966248545656204,0.126426626074589,3.63536360301136,0.629073015621382,0.0755781538580606,2.91670745952729,0.966248545656204,0.370926984378618,No PCV +Bogota.pre.PCV,7F,197,357200,4,0,3,adjusted_type_specific_negbin,0.00143409539618633,0.000284523665895276,0.00621858212124982,0.233250072846497,0.144992589116746,0.379897747934858,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,0.282516793048706,0.0560511621813693,1.22506067788621,4.5631619242246,0.999159345212585,19.0491276217905,0.282516793048706,1.5631619242246,PCV10 +Bogota.pre.PCV,8,197,357200,4,0,1,adjusted_type_specific_negbin,0.00230073214928302,0.000282314612379868,0.0101968690651182,0.233250072846497,0.144992589116746,0.379897747934858,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,0.453244233408755,0.055615978638834,2.00878320582828,1.45877779688336,0.187762531001045,6.46577521219891,0.453244233408755,0.458777796883361,PCV20 +Bogota.pre.PCV,9N,197,357200,4,5,2,adjusted_type_specific_negbin,0.0239955703442853,0.00975878290669025,0.0496020584293875,0.233250072846497,0.144992589116746,0.379897747934858,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,4.72712735782421,1.92248023261798,9.77160551058934,4.14094538486208,1.44542201709129,11.501522140485,0.272872642175789,2.14094538486208,PPV23 +Bogota.pre.PCV,9V,197,357200,4,0,8,adjusted_type_specific_negbin,0.00856632530887553,0.00296449402619077,0.0217471930837656,0.233250072846497,0.144992589116746,0.379897747934858,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,1.68756608584848,0.584005323159582,4.28419703750182,5.83878987870318,2.16856697813539,15.0690859845778,1.68756608584848,2.16121012129682,PCV7 +Caracas.pre.PCV,1,1004,146125,1,0,2,adjusted_type_specific_negbin,0.000829104218161101,0.000158010367539231,0.00295764744502494,0.902465436711435,0.471337543149167,1.78638528410582,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,0.832420635033745,0.158642409009388,2.96947803480504,1.90015068531573,0.370449232821634,6.86643566933169,0.832420635033745,0.0998493146842683,PCV10 +Caracas.pre.PCV,14,1004,146125,1,23,6,adjusted_type_specific_negbin,0.022229432354816,0.0146185266597326,0.0321974695477771,0.902465436711435,0.471337543149167,1.78638528410582,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,22.3183500842353,14.6770007663715,32.3262594259682,12.4221727307724,6.02496740097392,26.2174160516773,0.681649915764741,6.42217273077243,PCV7 +Caracas.pre.PCV,19A,1004,146125,1,32,3,adjusted_type_specific_negbin,0.0313675258250807,0.0220227195863066,0.0431452029633924,0.902465436711435,0.471337543149167,1.78638528410582,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,31.4929959283811,22.1108104646518,43.3177837752459,6.41717917316649,3.19858372378599,13.1255117892654,0.507004071618947,3.41717917316649,PCV13 +Caracas.pre.PCV,19F,1004,146125,1,3,2,adjusted_type_specific_negbin,0.00502223323110576,0.00195661771528623,0.010391748784405,0.902465436711435,0.471337543149167,1.78638528410582,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,5.04232216403018,1.96444418614738,10.4333157795426,0.424791894235004,0.140521799357855,1.13619842343145,2.04232216403018,1.575208105765,PCV7 +Caracas.pre.PCV,23F,1004,146125,1,25,1,adjusted_type_specific_negbin,0.0247732347207942,0.0165094238938458,0.0353917434083617,0.902465436711435,0.471337543149167,1.78638528410582,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,24.8723276596774,16.5754615894212,35.5333103819952,2.2646887685683,1.04992916052708,4.84550950173807,0.127672340322594,1.2646887685683,PCV7 +Caracas.pre.PCV,3,1004,146125,1,2,1,adjusted_type_specific_negbin,0.00285554032809557,0.000841384355553583,0.0069443602978916,0.902465436711435,0.471337543149167,1.78638528410582,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,2.86696248940795,0.844749892975797,6.97213773908316,0.768335462646709,0.200666648690538,2.26109333489785,0.866962489407954,0.231664537353291,PCV13 +Caracas.pre.PCV,4,1004,146125,1,3,0,adjusted_type_specific_negbin,0.00299695035435087,0.000874445360357515,0.0074969974186705,0.902465436711435,0.471337543149167,1.78638528410582,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,3.00893815576827,0.877943141798945,7.52698540834518,0.756245897800866,0.188746727154725,2.43270840891891,0.00893815576826906,0.756245897800866,PCV7 +Caracas.pre.PCV,5,1004,146125,1,0,2,adjusted_type_specific_negbin,0.00125891468890234,0.000254787410706673,0.00399588327460371,0.902465436711435,0.471337543149167,1.78638528410582,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,1.26395034765795,0.2558065603495,4.01186680770213,1.20363982787141,0.241492531263447,4.44906761690227,1.26395034765795,0.796360172128591,PCV10 +Caracas.pre.PCV,6A,1004,146125,1,20,3,adjusted_type_specific_negbin,0.0218102302426353,0.0141138814654785,0.0318635488756655,0.902465436711435,0.471337543149167,1.78638528410582,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,21.8974711636058,14.1703369913404,31.9910030711681,1.24791349618574,0.581577965230524,2.68074068303136,1.89747116360582,1.75208650381426,PCV13 +Caracas.pre.PCV,6B,1004,146125,1,70,10,adjusted_type_specific_negbin,0.0711174258310373,0.0564897205230824,0.0880236590528132,0.902465436711435,0.471337543149167,1.78638528410582,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,71.4018955343615,56.7156794051748,88.3757536890245,7.05423016471752,3.6965248502887,13.7257435051262,1.40189553436149,2.94576983528248,PCV7 +Caracas.pre.PCV,7F,1004,146125,1,1,3,adjusted_type_specific_negbin,0.00201738024728216,0.000588610670786124,0.00537416324495235,0.902465436711435,0.471337543149167,1.78638528410582,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,2.02544976827129,0.590965113469268,5.39565989793216,2.53122236235678,0.739851705797454,7.33626712392742,1.02544976827129,0.468777637643222,PCV10 +Caracas.pre.PCV,9V,1004,146125,1,2,0,adjusted_type_specific_negbin,0.0021608143907054,0.000483139565738428,0.00602820368917041,0.902465436711435,0.471337543149167,1.78638528410582,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,2.16945764826822,0.485072124001381,6.05231650392709,0.580734784175002,0.118906203310474,2.01802728718337,0.169457648268221,0.580734784175002,PCV7 +Czech.pre.PCV,1,425,478177,9,0,9,adjusted_type_specific_negbin,0.00165878959393703,0.000477923828742021,0.00534092234468666,0.0838886198099192,0.0506473389044988,0.14232456585829,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,0.704985577423239,0.203117627215359,2.26989199649183,10.2880948299628,3.43096656237349,32.0456916705849,0.704985577423239,1.28809482996284,PCV10 +Czech.pre.PCV,10A,425,478177,9,6,4,adjusted_type_specific_negbin,0.0157469680566988,0.00744743794341471,0.0292464030186936,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,6.69246142409698,3.16516112595125,12.4297212829448,4.05918130222672,1.75132179112155,9.11466256651486,0.69246142409698,0.0591813022267225,PCV20 +Czech.pre.PCV,11A,425,478177,9,8,1,adjusted_type_specific_negbin,0.0212231955104046,0.0105203076485002,0.0374909864489108,0.0838886198099192,0.0506473389044988,0.14232456585829,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,9.01985809192195,4.4711307506126,15.9336692407871,0.510826538952099,0.184301257464916,1.28874879255373,1.01985809192195,0.489173461047901,PCV20 +Czech.pre.PCV,12F,425,478177,9,0,1,adjusted_type_specific_negbin,0.000775147917482173,9.01310380061889e-05,0.00385289017720964,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00604185287379925,0.00279991943562254,0.0141061491643519,3.54240797176599,2.49560124043154,5.15073328448319,0.329437864929923,0.0383056911526303,1.6374783253141,1.69654780863823,0.216960502256733,8.16660641646839,0.329437864929923,0.696547808638226,PCV20 +Czech.pre.PCV,14,425,478177,9,5,19,adjusted_type_specific_negbin,0.0133810469505773,0.00646329771430213,0.025610583221285,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,5.68694495399534,2.74690152857841,10.8844978690461,20.3393252600486,9.50395698145079,43.1710311541626,0.686944953995336,1.33932526004862,PCV7 +Czech.pre.PCV,15B/C,425,478177,9,17,0,adjusted_type_specific_negbin,0.0368562830922747,0.0218515464827453,0.057425173810032,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,15.6639203142168,9.28690725516677,24.4056988692636,4.64234807431086,2.18898292998135,9.53933657885532,1.33607968578324,4.64234807431086,PCV20 +Czech.pre.PCV,17F,425,478177,9,0,1,adjusted_type_specific_negbin,0.00285865359407989,0.000408566785005146,0.00978256015581795,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,1.21492777748395,0.173640883627187,4.15758806622263,0.389894754043887,0.0534537736488333,1.57874314149915,1.21492777748395,0.610105245956113,PPV23 +Czech.pre.PCV,18C,425,478177,9,9,9,adjusted_type_specific_negbin,0.0192975835987417,0.00976840563099789,0.0344600225843681,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,8.20147302946523,4.1515723931741,14.6455095983565,18.7926016572759,8.46089326141753,42.4477236211529,0.798526970534766,9.79260165727586,PCV7 +Czech.pre.PCV,19A,425,478177,9,0,2,adjusted_type_specific_negbin,0.00262215785043015,0.000540927272312767,0.00834309251129621,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,1.11441708643282,0.229894090732926,3.54581431730089,1.46453208975171,0.311079871256381,4.69507966744274,1.11441708643282,0.535467910248286,PCV13 +Czech.pre.PCV,19F,425,478177,9,10,12,adjusted_type_specific_negbin,0.0292739275068656,0.017354234221299,0.046278801702584,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,12.4414191904179,7.37554954405209,19.6684907235982,6.78610094860228,3.59126983185412,12.7644532709064,2.44141919041788,5.21389905139772,PCV7 +Czech.pre.PCV,23A,425,478177,9,3,1,adjusted_type_specific_negbin,0.0095057045105531,0.00326124500775282,0.0209837453463569,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,4.03992441698507,1.38602912829495,8.9180917722017,0.538282942899377,0.158738717404819,1.50375398162739,1.03992441698507,0.461717057100623,No PCV +Czech.pre.PCV,23F,425,478177,9,30,13,adjusted_type_specific_negbin,0.0705559430111045,0.0494504380197847,0.0965870449410683,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,29.9862757797194,21.0164361584085,41.049494099954,17.5895692713048,9.64675484790511,32.3921749675749,0.0137242202805794,4.58956927130479,PCV7 +Czech.pre.PCV,28F,425,478177,9,0,2,adjusted_type_specific_negbin,0.00356033255095634,0.000581916564851083,0.0119575909374058,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000629505977950964,5.89638935363083e-05,0.00546065442840025,3.54240797176599,2.49560124043154,5.15073328448319,1.51314133415644,0.24731454006171,5.08197614839747,0.788979740797648,0.0817971032093261,4.27639484415247,1.51314133415644,1.21102025920235,No PCV +Czech.pre.PCV,3,425,478177,9,6,5,adjusted_type_specific_negbin,0.0130624761006191,0.00587973469572486,0.025415529733748,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,5.55155234276311,2.49888724568307,10.8016001368429,9.4874473885986,4.05914871901155,22.0552794383607,0.448447657236892,4.4874473885986,PCV13 +Czech.pre.PCV,33F,425,478177,9,0,1,adjusted_type_specific_negbin,0.00186575750125526,0.000239056683292258,0.00713430194457433,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,0.792946938033485,0.10159909039921,3.03207832644409,0.896719522726036,0.119469717251242,3.5991092132774,0.792946938033485,0.103280477273964,PCV15 +Czech.pre.PCV,35F,425,478177,9,5,0,adjusted_type_specific_negbin,0.0120094559632274,0.00459830292287114,0.0247051871316054,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,5.10401878437163,1.95427874222024,10.4997045309323,0.640295955733748,0.189567006662489,1.84738120273099,0.104018784371634,0.640295955733748,No PCV +Czech.pre.PCV,37,425,478177,9,2,1,adjusted_type_specific_negbin,0.00768898756629687,0.00222670201384814,0.0187085058188017,0.0838886198099192,0.0506473389044988,0.14232456585829,8.73857936299313e-05,4.08275642783979e-06,0.000582177503837751,3.54240797176599,2.49560124043154,5.15073328448319,3.26781971567617,0.946348355885461,7.95111497299074,0.232655727900743,0.0107135099850503,1.58604878540213,1.26781971567617,0.767344272099257,No PCV +Czech.pre.PCV,38,425,478177,9,1,1,adjusted_type_specific_negbin,0.0036929965578394,0.000798643759427354,0.0109661392711757,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,1.56952353708174,0.339423597756626,4.66060919024965,1.15484154237279,0.237637135150004,4.07433707636938,0.569523537081744,0.154841542372789,No PCV +Czech.pre.PCV,4,425,478177,9,2,5,adjusted_type_specific_negbin,0.00685982483853436,0.00251845122259601,0.0158493639414768,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,2.9154255563771,1.0703417696033,6.73597967512765,4.68451423543688,1.74512950346856,11.9682963341155,0.915425556377104,0.31548576456312,PCV7 +Czech.pre.PCV,40,425,478177,9,0,1,adjusted_type_specific_negbin,0.00165808094966104,6.4176013230772e-05,0.00855519210698777,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00133846997461256,2.80248334452259e-05,0.0582094968249939,3.54240797176599,2.49560124043154,5.15073328448319,0.704684403605944,0.0272748056230781,3.6359566454698,0.766088375079043,0.0240230110276493,6.39301300043175,0.704684403605944,0.233911624920957,No PCV +Czech.pre.PCV,5,425,478177,9,0,1,adjusted_type_specific_negbin,0.000685516508626158,7.41100807992859e-05,0.00355607738002083,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,0.291344516166117,0.0314967843396965,1.51133288650885,1.79241112413262,0.220349844710401,9.07235206389305,0.291344516166117,0.792411124132621,PCV10 +Czech.pre.PCV,6A,425,478177,9,24,8,adjusted_type_specific_negbin,0.0574728063934809,0.0386305509025855,0.08122187474658,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,24.4259427172294,16.4179841335988,34.5192967672965,8.95356617253496,4.88011415944726,16.8574267448635,0.425942717229397,0.953566172534956,PCV13 +Czech.pre.PCV,6B,425,478177,9,21,23,adjusted_type_specific_negbin,0.0545924059101516,0.0368217988206442,0.0776850667549325,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,23.2017725118144,15.6492644987738,33.0161533708463,14.7099165988036,8.42460934983092,26.4869441155938,2.20177251181443,8.29008340119644,PCV7 +Czech.pre.PCV,7F,425,478177,9,1,6,adjusted_type_specific_negbin,0.00261273815065437,0.000759602937023074,0.00783102189500036,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,1.11041371402811,0.322831248234807,3.32818430537515,8.90385366308348,2.82747761381039,27.5595583351473,0.110413714028108,2.90385366308348,PCV10 +Czech.pre.PCV,8,425,478177,9,1,1,adjusted_type_specific_negbin,0.0027492943004147,0.000561954998762924,0.00882392157212154,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,1.16845007767625,0.238830874474243,3.75016666815166,1.88681389049434,0.390010321521846,6.68669605018304,0.168450077676246,0.886813890494343,PCV20 +Czech.pre.PCV,9N,425,478177,9,1,2,adjusted_type_specific_negbin,0.00559783978187425,0.00158590846875591,0.0143099068543169,0.0838886198099192,0.0506473389044988,0.14232456585829,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,2.37908190729656,0.674011099221263,6.08171041308467,1.05219948182318,0.267376009348406,3.34364835631732,1.37908190729656,0.947800518176819,PPV23 +Czech.pre.PCV,9V,425,478177,9,1,9,adjusted_type_specific_negbin,0.00748026333815579,0.00299255518215848,0.0163458137148264,0.0838886198099192,0.0506473389044988,0.14232456585829,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,3.17911191871621,1.27183595241735,6.94697082880121,5.50444182407202,2.2987880099791,12.9300936654726,2.17911191871621,3.49555817592798,PCV7 +France.post.PCV7,1,1212,838866,2,2,30,adjusted_type_specific_negbin,0.00140971255000793,0.000498137930933771,0.00378744080729785,1.20736274678871,0.779648488568653,1.89346039828249,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,1.70857161060962,0.60374317229173,4.59037825844499,48.594580447013,18.5043753152152,139.318426625193,0.291428389390384,18.594580447013,PCV10 +France.post.PCV7,10A,1212,838866,2,0,7,adjusted_type_specific_negbin,0.0022460587052126,0.000842991629747032,0.00512005665041091,1.20736274678871,0.779648488568653,1.89346039828249,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,2.72222315071767,1.0217058552534,6.20550866029802,3.25902180469695,1.2509413259459,7.70117199932222,2.72222315071767,3.74097819530305,PCV20 +France.post.PCV7,10B,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000713059649461377,9.10949140191343e-05,0.00283247387929901,1.20736274678871,0.779648488568653,1.89346039828249,0.000509389844494032,8.66360486448286e-05,0.00249463469166522,3.54240797176599,2.49560124043154,5.15073328448319,0.864228295147189,0.110407035791191,3.43295834171039,0.714356143809714,0.0763461651214088,3.81629651098357,0.864228295147189,0.285643856190286,No PCV +France.post.PCV7,11A,1212,838866,2,10,1,adjusted_type_specific_negbin,0.0086817103936821,0.00463931812970235,0.0147706884330314,1.20736274678871,0.779648488568653,1.89346039828249,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,10.5222329971427,5.62285357319924,17.9020743808341,1.1798442887153,0.466953667231932,2.7476538022792,0.522232997142709,0.179844288715301,PCV20 +France.post.PCV7,12B,1212,838866,2,1,1,adjusted_type_specific_negbin,0.00101454787325158,0.000146295270621879,0.00364094609584388,1.20736274678871,0.779648488568653,1.89346039828249,0.000811154229848642,7.42387102385189e-05,0.00720154276127019,3.54240797176599,2.49560124043154,5.15073328448319,1.22963202238091,0.177309867993717,4.41282666816278,1.57124244632432,0.172486145801773,9.52510457546933,0.229632022380911,0.571242446324325,No PCV +France.post.PCV7,12F,1212,838866,2,0,9,adjusted_type_specific_negbin,0.000760313533412368,0.000212365972412162,0.00235859807168525,1.20736274678871,0.779648488568653,1.89346039828249,0.00604185287379925,0.00279991943562254,0.0141061491643519,3.54240797176599,2.49560124043154,5.15073328448319,0.92150000249579,0.25738755856354,2.85862086288252,9.14744625533573,3.19019741805835,27.5806510515638,0.92150000249579,0.147446255335733,PCV20 +France.post.PCV7,14,1212,838866,2,0,6,adjusted_type_specific_negbin,0.000721722899705334,0.000219745742896149,0.00221502748738156,1.20736274678871,0.779648488568653,1.89346039828249,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,0.874728154442864,0.266331840390133,2.68461331470645,6.17160514417203,1.9579376203595,18.8001984182686,0.874728154442864,0.171605144172029,PCV7 +France.post.PCV7,15A,1212,838866,2,13,6,adjusted_type_specific_negbin,0.0106435983087108,0.00616544363228026,0.0172013130399534,1.20736274678871,0.779648488568653,1.89346039828249,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,12.9000411501575,7.47251768232368,20.8479914044236,8.96380625486954,4.20772527403238,19.1459689352428,0.0999588498424924,2.96380625486954,No PCV +France.post.PCV7,15B/C,1212,838866,2,23,17,adjusted_type_specific_negbin,0.0200817542767884,0.0135337137099427,0.0284693638288806,1.20736274678871,0.779648488568653,1.89346039828249,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,24.3390861834676,16.4028610164505,34.5048689606033,14.1123732697436,7.95453061857825,25.3272024619073,1.33908618346755,2.88762673025644,PCV20 +France.post.PCV7,15F,1212,838866,2,1,0,adjusted_type_specific_negbin,0.00107425962782826,0.000153501193099844,0.00374350348918067,1.20736274678871,0.779648488568653,1.89346039828249,0.000170123300166289,2.02083655214776e-05,0.000864026455062348,3.54240797176599,2.49560124043154,5.15073328448319,1.30200266892785,0.186043446037011,4.53712622888697,0.350996797923665,0.0264390013514071,2.25189557111574,0.30200266892785,0.350996797923665,No PCV +France.post.PCV7,16F,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000814399742373176,0.000112098507045693,0.00297868903552999,1.20736274678871,0.779648488568653,1.89346039828249,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,0.98705248775629,0.13586339053938,3.61017111106234,0.650235827233373,0.0860717443344499,2.55894737548839,0.98705248775629,0.349764172766627,No PCV +France.post.PCV7,17F,1212,838866,2,4,4,adjusted_type_specific_negbin,0.0042257067108841,0.00181597346193384,0.0083718333083188,1.20736274678871,0.779648488568653,1.89346039828249,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,5.12155653359153,2.20095983586381,10.1466619696824,3.24272167196459,1.23414858381384,8.0186582636372,1.12155653359153,0.757278328035406,PPV23 +France.post.PCV7,18A,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000975613477357902,0.000128525614555674,0.00358856698907975,1.20736274678871,0.779648488568653,1.89346039828249,0.000198001510080884,2.43125238691192e-05,0.000991711750205049,3.54240797176599,2.49560124043154,5.15073328448319,1.18244353455778,0.155773044841476,4.34934319076466,0.365704286784624,0.0303101703338881,2.17493838064943,1.18244353455778,0.634295713215376,No PCV +France.post.PCV7,18C,1212,838866,2,0,2,adjusted_type_specific_negbin,0.000450680166573661,7.98957835531127e-05,0.00176346846264172,1.20736274678871,0.779648488568653,1.89346039828249,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,0.546224361887278,0.0968336896663726,2.13732377672176,2.48070959533138,0.487683860925462,9.52062726496067,0.546224361887278,0.48070959533138,PCV7 +France.post.PCV7,19A,1212,838866,2,28,128,adjusted_type_specific_negbin,0.0254050561341519,0.0180185341096539,0.0346310046677345,1.20736274678871,0.779648488568653,1.89346039828249,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,30.7909280345921,21.8384633409005,41.9727776572942,79.592230070999,49.5039918651403,129.174756584077,2.79092803459213,48.407769929001,PCV13 +France.post.PCV7,19F,1212,838866,2,8,10,adjusted_type_specific_negbin,0.00732840901950834,0.00396917035126223,0.012577409535313,1.20736274678871,0.779648488568653,1.89346039828249,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,8.88203173164411,4.81063446572982,15.2438203567993,9.52563936195829,4.7459452868835,18.803559215798,0.882031731644108,0.474360638041709,PCV7 +France.post.PCV7,20,1212,838866,2,1,0,adjusted_type_specific_negbin,0.000709262596509083,8.65438210968995e-05,0.00281645751617944,1.20736274678871,0.779648488568653,1.89346039828249,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,0.859626266969009,0.104891111169442,3.41354650960949,1.06840394530709,0.123467739721065,5.31281009802833,0.140373733030991,1.06840394530709,PPV23 +France.post.PCV7,21,1212,838866,2,11,3,adjusted_type_specific_negbin,0.0093211199163228,0.00515395522775737,0.0154613390617725,1.20736274678871,0.779648488568653,1.89346039828249,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,11.2971973385832,6.24659373604194,18.7391429428683,3.73965627108581,1.48673631279941,8.88556453220316,0.297197338583235,0.739656271085809,No PCV +France.post.PCV7,22F,1212,838866,2,3,6,adjusted_type_specific_negbin,0.00304413199082956,0.00122433865601891,0.00656140075268349,1.20736274678871,0.779648488568653,1.89346039828249,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,3.68948797288542,1.48389845109491,7.95241771225239,6.29346582006385,2.51595421074584,15.010180165639,0.689487972885421,0.293465820063847,PCV15 +France.post.PCV7,23A,1212,838866,2,8,2,adjusted_type_specific_negbin,0.00704199206041321,0.00350953044145327,0.0123769255646458,1.20736274678871,0.779648488568653,1.89346039828249,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,8.53489437722081,4.25355089504137,15.0008337843507,2.24577737459262,0.930019753324386,5.10221746256585,0.534894377220809,0.24577737459262,No PCV +France.post.PCV7,23B,1212,838866,2,10,3,adjusted_type_specific_negbin,0.0083469619844611,0.00444454043520224,0.0142440780347504,1.20736274678871,0.779648488568653,1.89346039828249,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,10.1165179251668,5.38678300746511,17.2638225781175,4.34365732100483,1.96072396664315,9.28920933003117,0.116517925166846,1.34365732100483,No PCV +France.post.PCV7,23F,1212,838866,2,3,2,adjusted_type_specific_negbin,0.00248170026112583,0.000854103409926837,0.00577266266784544,1.20736274678871,0.779648488568653,1.89346039828249,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,3.00782071648451,1.03517333283133,6.99646715342867,3.45287842467461,1.16933274166884,8.95716369563377,0.00782071648450877,1.45287842467461,PCV7 +France.post.PCV7,24B,1212,838866,2,0,3,adjusted_type_specific_negbin,0.000493178878265404,4.17055081185133e-05,0.00250357117894294,1.20736274678871,0.779648488568653,1.89346039828249,0.00341769534218185,0.000432780069399651,0.0397781644729013,3.54240797176599,2.49560124043154,5.15073328448319,0.597732800457669,0.0505470758396381,3.03432826887885,3.24939242567535,0.678167899414433,15.4707599491352,0.597732800457669,0.249392425675348,No PCV +France.post.PCV7,24F,1212,838866,2,2,25,adjusted_type_specific_negbin,0.00370029377227605,0.00165381821837748,0.00732009075165647,1.20736274678871,0.779648488568653,1.89346039828249,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,4.48475605199857,2.0044276806735,8.87194999100764,16.2508975129564,7.80419594710321,35.3171398036295,2.48475605199857,8.74910248704359,No PCV +France.post.PCV7,25A,1212,838866,2,0,15,adjusted_type_specific_negbin,0.0024476259409324,0.000863773335130114,0.00568697257075991,1.20736274678871,0.779648488568653,1.89346039828249,0.00165141051651395,0.000589976401575755,0.00500660807717493,3.54240797176599,2.49560124043154,5.15073328448319,2.96652264041007,1.0468932821777,6.89261075576101,7.97584681776956,3.42816840544819,19.8430567501652,2.96652264041007,7.02415318223044,No PCV +France.post.PCV7,28F,1212,838866,2,1,0,adjusted_type_specific_negbin,0.000743295943008105,7.69397662551323e-05,0.00308551752187093,1.20736274678871,0.779648488568653,1.89346039828249,0.000629505977950964,5.89638935363083e-05,0.00546065442840025,3.54240797176599,2.49560124043154,5.15073328448319,0.900874682925823,0.0932509967012203,3.73964723650756,0.897899243427309,0.0702814159874942,6.12894425917331,0.0991253170741768,0.897899243427309,No PCV +France.post.PCV7,29,1212,838866,2,3,0,adjusted_type_specific_negbin,0.00268557374623735,0.000756508082399267,0.00663916707126753,1.20736274678871,0.779648488568653,1.89346039828249,6.39161619681567e-05,3.15448575829138e-06,0.000496397918354293,3.54240797176599,2.49560124043154,5.15073328448319,3.25491538043967,0.916887795867912,8.04667049037624,0.33476584590246,0.015986043608856,2.53958773376435,0.254915380439672,0.33476584590246,No PCV +France.post.PCV7,3,1212,838866,2,1,18,adjusted_type_specific_negbin,0.00282022752416405,0.00125782691451977,0.005804851075442,1.20736274678871,0.779648488568653,1.89346039828249,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,3.41811575928682,1.52448622039796,7.03547950343571,11.5350473118383,5.40481290459374,24.7780467280867,2.41811575928682,6.46495268816175,PCV13 +France.post.PCV7,31,1212,838866,2,0,2,adjusted_type_specific_negbin,0.00113152450135034,0.000235224857396517,0.00350905158906965,1.20736274678871,0.779648488568653,1.89346039828249,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,1.37140769563661,0.285092527164578,4.25297052595241,1.07577457476727,0.212160112369326,3.96863342346332,1.37140769563661,0.924225425232731,No PCV +France.post.PCV7,33F,1212,838866,2,3,5,adjusted_type_specific_negbin,0.00258946222028376,0.000972091321190591,0.00586566004007667,1.20736274678871,0.779648488568653,1.89346039828249,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,3.13842821098392,1.178174681283,7.10917996857293,6.93389797784183,2.62823935226201,17.8592790401316,0.138428210983915,1.93389797784183,PCV15 +France.post.PCV7,34,1212,838866,2,1,0,adjusted_type_specific_negbin,0.00118407712618174,0.000169499267748502,0.00396436982527696,1.20736274678871,0.779648488568653,1.89346039828249,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,1.43510147693227,0.205433112511185,4.80481622823568,0.22644789070184,0.0229187400859869,1.2056707642639,0.435101476932271,0.22644789070184,No PCV +France.post.PCV7,35B,1212,838866,2,8,1,adjusted_type_specific_negbin,0.00674135457439098,0.00327709176196138,0.0121248063214792,1.20736274678871,0.779648488568653,1.89346039828249,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,8.17052174416187,3.97183521549719,14.6952652616328,1.76269720909735,0.633917951134145,4.34380260275879,0.170521744161874,0.762697209097354,No PCV +France.post.PCV7,35F,1212,838866,2,7,3,adjusted_type_specific_negbin,0.00682047731986595,0.00335553521242229,0.012137400121367,1.20736274678871,0.779648488568653,1.89346039828249,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,8.26641851167754,4.06690867745582,14.7105289470969,2.04521193801786,0.77129020179579,5.00441051684271,1.26641851167754,0.954788061982137,No PCV +France.post.PCV7,4,1212,838866,2,2,0,adjusted_type_specific_negbin,0.000870330421941977,0.000166919013816663,0.00306116604442452,1.20736274678871,0.779648488568653,1.89346039828249,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,1.05484047139368,0.202305844745796,3.71013324584252,3.36594292408771,0.632156399575053,12.8540927291062,0.945159528606324,3.36594292408771,PCV7 +France.post.PCV7,45,1212,838866,2,1,0,adjusted_type_specific_negbin,0.00125302879737611,0.000166885223516617,0.00425629601391552,1.20736274678871,0.779648488568653,1.89346039828249,1.60690114347185e-05,1.1309785447003e-06,0.000842725740828315,3.54240797176599,2.49560124043154,5.15073328448319,1.51867090241985,0.20226489090214,5.15863076886561,0.0404765545049724,0.00150753799258067,1.62537937346714,0.518670902419845,0.0404765545049724,No PCV +France.post.PCV7,46,1212,838866,2,0,1,adjusted_type_specific_negbin,2.77801795902303e-05,1.06229454854362e-06,0.000426481865576877,1.20736274678871,0.779648488568653,1.89346039828249,0.0442990863665676,0.00447299728729766,0.570835275093796,3.54240797176599,2.49560124043154,5.15073328448319,0.0336695776633592,0.00128750099283487,0.516896021079175,2.46951089765105,0.284978262492745,17.4387719643525,0.0336695776633592,1.46951089765105,No PCV +France.post.PCV7,5,1212,838866,2,0,4,adjusted_type_specific_negbin,0.000360697388648738,7.05583881737398e-05,0.00147772067365201,1.20736274678871,0.779648488568653,1.89346039828249,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,0.437165235042271,0.0855167664665726,1.79099745646623,5.30291760030603,1.31692516667985,20.5927328982971,0.437165235042271,1.30291760030603,PCV10 +France.post.PCV7,6A,1212,838866,2,10,3,adjusted_type_specific_negbin,0.00774793175494394,0.00408826978614653,0.0133832950866507,1.20736274678871,0.779648488568653,1.89346039828249,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,9.39049328699205,4.95498298080959,16.2205536450207,6.77254382552397,3.22040420151402,13.9334746399346,0.609506713007949,3.77254382552397,PCV13 +France.post.PCV7,6B,1212,838866,2,3,4,adjusted_type_specific_negbin,0.00294257939130976,0.00114571008456143,0.00644989506525837,1.20736274678871,0.779648488568653,1.89346039828249,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,3.56640622226743,1.38860062248846,7.81727281909314,4.44118453931708,1.70405548562263,10.5019687228088,0.566406222267434,0.441184539317082,PCV7 +France.post.PCV7,6C,1212,838866,2,13,4,adjusted_type_specific_negbin,0.0122358487750763,0.00723846273634723,0.0192447891607314,1.20736274678871,0.779648488568653,1.89346039828249,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,14.8298487153925,8.77301683645284,23.3246844628064,2.05757523127914,0.801799126065478,4.92059801178072,1.82984871539249,1.94242476872086,No PCV +France.post.PCV7,7C,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000794972154649676,0.000106089106582994,0.00303620847696731,1.20736274678871,0.779648488568653,1.89346039828249,0.000395968078807268,0.000112206548547661,0.00124464123083086,3.54240797176599,2.49560124043154,5.15073328448319,0.963506251435407,0.128579997178589,3.67988467408437,0.617268106458572,0.0761159347847791,2.77383358286475,0.963506251435407,0.382731893541428,No PCV +France.post.PCV7,7F,1212,838866,2,2,53,adjusted_type_specific_negbin,0.00263424016306327,0.00114127598365271,0.00557754301876883,1.20736274678871,0.779648488568653,1.89346039828249,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,3.19269907763269,1.38322649218708,6.75998213874782,50.0535346851703,23.3940379249956,112.812890897186,1.19269907763269,2.94646531482972,PCV10 +France.post.PCV7,8,1212,838866,2,1,1,adjusted_type_specific_negbin,0.000695040699447671,0.000131036495647436,0.00252339369978082,1.20736274678871,0.779648488568653,1.89346039828249,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,0.842389327730577,0.158816232724692,3.05835316413435,2.67534190088174,0.531143616339538,10.2482990847899,0.157610672269423,1.67534190088174,PCV20 +France.post.PCV7,9A,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000790088332424722,7.78703825812021e-05,0.00341178102749075,1.20736274678871,0.779648488568653,1.89346039828249,0.000335225096715175,1.03750856015762e-05,0.00445225735285593,3.54240797176599,2.49560124043154,5.15073328448319,0.957587058898763,0.0943789036884169,4.13507860531879,0.499536753880696,0.0183525527678884,3.93075435590966,0.957587058898763,0.500463246119304,No PCV +France.post.PCV7,9L,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000286289571139608,1.39308815648505e-05,0.00202903600683745,1.20736274678871,0.779648488568653,1.89346039828249,0.00268938450687417,0.000175749113163652,0.039503533475621,3.54240797176599,2.49560124043154,5.15073328448319,0.346982960221205,0.0168842284565988,2.45919164028698,1.43113054055582,0.141064662043671,9.17483421890979,0.346982960221205,0.431130540555823,No PCV +France.post.PCV7,9N,1212,838866,2,1,1,adjusted_type_specific_negbin,0.00122362472839146,0.000259036596859526,0.00372560479189916,1.20736274678871,0.779648488568653,1.89346039828249,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,1.48303317081045,0.313952355393746,4.51543300778178,1.29655140405979,0.261796638348964,4.52386849935162,0.483033170810454,0.29655140405979,PPV23 +France.post.PCV7,9V,1212,838866,2,0,2,adjusted_type_specific_negbin,0.000543332602287015,0.00010060130712752,0.00201754962860823,1.20736274678871,0.779648488568653,1.89346039828249,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,0.658519113971862,0.121928784238554,2.44527014987318,2.25715891574072,0.447862783253754,8.35246658020298,0.658519113971862,0.257158915740725,PCV7 +Goroka.pre.PCV,1,2844,96207,6,1,1,adjusted_type_specific_negbin,0.000671089811843036,0.000150867652600645,0.00190385123682101,0.107811836825013,0.0458312125109177,0.249382816095641,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,1.9085794248816,0.429067603996235,5.41455291751896,0.716396211723065,0.144514643976801,2.50503045388621,0.908579424881596,0.283603788276935,PCV10 +Goroka.pre.PCV,13,2844,96207,6,45,1,adjusted_type_specific_negbin,0.0161431199621812,0.0119798856452786,0.0210877972672243,0.107811836825013,0.0458312125109177,0.249382816095641,0.000641136431718939,0.000181165818687303,0.00210187050439682,3.54240797176599,2.49560124043154,5.15073328448319,45.9110331724433,34.0707947751724,59.9736954279859,0.643746573708808,0.16340248329337,2.29001902848949,0.911033172443332,0.356253426291192,No PCV +Goroka.pre.PCV,14,2844,96207,6,118,7,adjusted_type_specific_negbin,0.0413740760467573,0.0345647817062799,0.0491510941917944,0.107811836825013,0.0458312125109177,0.249382816095641,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,117.667872276978,98.3022391726601,139.785711881463,10.9202627958141,4.78670931956441,25.0609502999771,0.332127723022253,3.9202627958141,PCV7 +Goroka.pre.PCV,2,2844,96207,6,2,1,adjusted_type_specific_negbin,0.00110706239363367,0.000305956219897712,0.00278742476986507,0.107811836825013,0.0458312125109177,0.249382816095641,0.00396667808056597,0.000257626265044538,0.0519109501755693,3.54240797176599,2.49560124043154,5.15073328448319,3.14848544749416,0.870139489389093,7.92743604549625,0.278123777461073,0.0147446766245915,2.62867389802656,1.14848544749416,0.721876222538927,PPV23 +Goroka.pre.PCV,20,2844,96207,6,12,0,adjusted_type_specific_negbin,0.00435838770534895,0.00237633192107107,0.00727656527573589,0.107811836825013,0.0458312125109177,0.249382816095641,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,12.3952546340124,6.75828798352613,20.6945516441929,0.205579285811156,0.0430584895797781,0.857166131053515,0.395254634012417,0.205579285811156,PPV23 +Goroka.pre.PCV,21,2844,96207,6,45,0,adjusted_type_specific_negbin,0.0159931877940096,0.011839268044561,0.0209530106114744,0.107811836825013,0.0458312125109177,0.249382816095641,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,45.4846260861634,33.6708783187315,59.5903621790331,0.199476691707445,0.0629299346033752,0.597856185563396,0.48462608616336,0.199476691707445,No PCV +Goroka.pre.PCV,29,2844,96207,6,22,0,adjusted_type_specific_negbin,0.00794103048149805,0.00510388388948439,0.01163252719411,0.107811836825013,0.0458312125109177,0.249382816095641,6.39161619681567e-05,3.15448575829138e-06,0.000496397918354293,3.54240797176599,2.49560124043154,5.15073328448319,22.5842906893805,14.5154457816936,33.0829073400488,0.0308621177265277,0.00145002181500645,0.2779646332974,0.58429068938047,0.0308621177265277,No PCV +Goroka.pre.PCV,3,2844,96207,6,23,0,adjusted_type_specific_negbin,0.00803075560905942,0.005246627180188,0.0116993420665958,0.107811836825013,0.0458312125109177,0.249382816095641,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,22.839468952165,14.9214077004547,33.2729288373985,1.01647056810423,0.386948002844037,2.55774695233753,0.160531047835015,1.01647056810423,PCV13 +Goroka.pre.PCV,31,2844,96207,6,14,1,adjusted_type_specific_negbin,0.00541917414449573,0.00315336791954944,0.00858379550073398,0.107811836825013,0.0458312125109177,0.249382816095641,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,15.4121312669459,8.9681783631986,24.4123144040874,0.162712513659891,0.0418255760342102,0.576927383101441,1.41213126694585,0.837287486340109,No PCV +Goroka.pre.PCV,34,2844,96207,6,44,1,adjusted_type_specific_negbin,0.0159820255460726,0.0117725140674292,0.0211585305172365,0.107811836825013,0.0458312125109177,0.249382816095641,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,45.4528806530305,33.4810300077686,60.1748607910207,0.098153848579878,0.0177880626575091,0.405710850492127,1.45288065303045,0.901846151420122,No PCV +Goroka.pre.PCV,36,2844,96207,6,1,0,adjusted_type_specific_negbin,0.000585438648872891,8.4295520551551e-05,0.00197280937769814,0.107811836825013,0.0458312125109177,0.249382816095641,2.58839998099884e-05,1.1820498282222e-06,0.00170666709060845,3.54240797176599,2.49560124043154,5.15073328448319,1.6649875173945,0.239736460448611,5.61066987017351,0.000884027039954679,1.9686927630478e-05,0.0819861215103968,0.664987517394503,0.000884027039954679,No PCV +Goroka.pre.PCV,38,2844,96207,6,21,0,adjusted_type_specific_negbin,0.00747236693303311,0.00476710562935564,0.0110230966497608,0.107811836825013,0.0458312125109177,0.249382816095641,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,21.2514115575462,13.5576484098875,31.3496868719198,0.40634111189822,0.126300073693174,1.2538848224756,0.251411557546163,0.40634111189822,No PCV +Goroka.pre.PCV,39,2844,96207,6,4,0,adjusted_type_specific_negbin,0.00159976518255223,0.000547514657435377,0.00358084580470531,0.107811836825013,0.0458312125109177,0.249382816095641,8.13720832508607e-05,1.22435094066609e-06,0.0163443113911506,3.54240797176599,2.49560124043154,5.15073328448319,4.54973217917854,1.55713168574621,10.1839254685819,0.00816864766421738,9.11713687744887e-05,1.35538354203837,0.549732179178545,0.00816864766421738,No PCV +Goroka.pre.PCV,4,2844,96207,6,27,0,adjusted_type_specific_negbin,0.0094084566348217,0.00632745928098906,0.0133984443604061,0.107811836825013,0.0458312125109177,0.249382816095641,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,26.7576506694329,17.9952941951329,38.1051757609949,1.12843762383045,0.41360579451842,2.95255193595552,0.242349330567073,1.12843762383045,PCV7 +Goroka.pre.PCV,42,2844,96207,6,14,0,adjusted_type_specific_negbin,0.00514288250001954,0.00295195700701271,0.00817908736630489,0.107811836825013,0.0458312125109177,0.249382816095641,1.64727034476203e-05,1.1485247591461e-06,0.000721087752303597,3.54240797176599,2.49560124043154,5.15073328448319,14.6263578300556,8.39536572794414,23.2613244697711,0.00528348313800444,0.000276020049117243,0.252166105079057,0.626357830055579,0.00528348313800444,No PCV +Goroka.pre.PCV,43,2844,96207,6,1,0,adjusted_type_specific_negbin,0.000551094129052395,7.5685467712461e-05,0.00188951179828587,0.107811836825013,0.0458312125109177,0.249382816095641,0.000134550145824311,1.25458135568121e-06,0.0536979753199508,3.54240797176599,2.49560124043154,5.15073328448319,1.56731170302501,0.215249470174239,5.37377155432501,0.00457150153104439,2.54890679777435e-05,1.2401238462366,0.56731170302501,0.00457150153104439,No PCV +Goroka.pre.PCV,45,2844,96207,6,7,0,adjusted_type_specific_negbin,0.00269704078268495,0.00121782001790744,0.00505244654753782,0.107811836825013,0.0458312125109177,0.249382816095641,1.60690114347185e-05,1.1309785447003e-06,0.000842725740828315,3.54240797176599,2.49560124043154,5.15073328448319,7.67038398595601,3.46348013092876,14.3691579811976,0.00267134373807313,0.000133417537964641,0.147941341164943,0.670383985956008,0.00267134373807313,No PCV +Goroka.pre.PCV,46,2844,96207,6,0,3,adjusted_type_specific_negbin,0.000566205231534451,8.22668340583826e-05,0.00186805222676129,0.107811836825013,0.0458312125109177,0.249382816095641,0.0442990863665676,0.00447299728729766,0.570835275093796,3.54240797176599,2.49560124043154,5.15073328448319,1.61028767848398,0.23396687606204,5.31274053290911,1.51123328415235,0.22408334405108,7.70552566910508,1.61028767848398,1.48876671584765,No PCV +Goroka.pre.PCV,47,2844,96207,6,1,0,adjusted_type_specific_negbin,0.000555514291380549,7.65795987141549e-05,0.00184000472786602,0.107811836825013,0.0458312125109177,0.249382816095641,0.00013838424471484,1.23940863122508e-06,0.05562789912659,3.54240797176599,2.49560124043154,5.15073328448319,1.57988264468628,0.217792378743057,5.23297344605095,0.00474982840286976,2.4114166783877e-05,1.28445681987015,0.579882644686281,0.00474982840286976,No PCV +Goroka.pre.PCV,5,2844,96207,6,5,2,adjusted_type_specific_negbin,0.00223064663429838,0.000972258219728138,0.00435301696347328,0.107811836825013,0.0458312125109177,0.249382816095641,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,6.34395902794459,2.76510237690682,12.379980244118,1.01430678417248,0.292956510584194,3.19210486347951,1.34395902794459,0.985693215827518,PCV10 +Goroka.pre.PCV,8,2844,96207,6,9,0,adjusted_type_specific_negbin,0.00327027637928858,0.00162991867056739,0.0057415231245834,0.107811836825013,0.0458312125109177,0.249382816095641,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,9.30066602269672,4.63548869909366,16.3288917663152,0.38756874575661,0.114748648113179,1.22515746737254,0.300666022696717,0.38756874575661,PCV20 +Massachusetts.post.PCV7,1,2969,820000,3,0,1,adjusted_type_specific_negbin,0.000104948844820215,1.24946744289469e-05,0.000511083632804864,0.395262731662366,0.253462664196128,0.614675280443518,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,0.31159312027122,0.0370966883795434,1.51740730579764,1.76004656532439,0.221678022423717,8.39928442722374,0.31159312027122,0.760046565324394,PCV10 +Massachusetts.post.PCV7,10A,2969,820000,3,27,4,adjusted_type_specific_negbin,0.00904291787756756,0.00611991937824289,0.0127942252299961,0.395262731662366,0.253462664196128,0.614675280443518,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,26.8484231784981,18.1700406340031,37.9860547078585,6.31273322239387,3.30541292566709,12.0882572544699,0.151576821501919,2.31273322239387,PCV20 +Massachusetts.post.PCV7,11A,2969,820000,3,63,3,adjusted_type_specific_negbin,0.0217742897911389,0.0169528148421768,0.0274949713747547,0.395262731662366,0.253462664196128,0.614675280443518,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,64.6478663898913,50.332907266423,81.6325700116467,1.43171967989173,0.651546561409767,2.9151410067073,1.64786638989135,1.56828032010827,PCV20 +Massachusetts.post.PCV7,12B,2969,820000,3,0,1,adjusted_type_specific_negbin,0.000408370571947441,4.97964446681415e-05,0.00149241638058701,0.395262731662366,0.253462664196128,0.614675280443518,0.000811154229848642,7.42387102385189e-05,0.00720154276127019,3.54240797176599,2.49560124043154,5.15073328448319,1.21245222811195,0.147845644219712,4.43098423396284,0.312459572199186,0.0193664961497605,2.38895355544604,1.21245222811195,0.687540427800814,No PCV +Massachusetts.post.PCV7,13,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000467447443123489,6.72714848982368e-05,0.00158817785502438,0.395262731662366,0.253462664196128,0.614675280443518,0.000641136431718939,0.000181165818687303,0.00210187050439682,3.54240797176599,2.49560124043154,5.15073328448319,1.38785145863364,0.199729038662865,4.71530005156738,0.280519689723525,0.0316067424752219,1.41405562022337,0.387851458633639,0.280519689723525,No PCV +Massachusetts.post.PCV7,14,2969,820000,3,3,1,adjusted_type_specific_negbin,0.000848531481974937,0.000266304023754058,0.00207530150203225,0.395262731662366,0.253462664196128,0.614675280443518,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,2.51928996998359,0.790656646525797,6.16157015953374,3.47403478514936,1.0807273205976,9.15303667121249,0.480710030016411,2.47403478514936,PCV7 +Massachusetts.post.PCV7,15A,2969,820000,3,36,3,adjusted_type_specific_negbin,0.0121138510462345,0.00863871302256104,0.0163509329530149,0.395262731662366,0.253462664196128,0.614675280443518,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,35.9660237562702,25.6483389639837,48.5459199375013,4.90588818668029,2.43013686624449,9.86069984326921,0.0339762437297679,1.90588818668029,No PCV +Massachusetts.post.PCV7,15B/C,2969,820000,3,74,8,adjusted_type_specific_negbin,0.0250867050791395,0.0199908862353705,0.0310368695817319,0.395262731662366,0.253462664196128,0.614675280443518,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,74.4824273799653,59.352941232815,92.1484657881621,8.5234508059937,4.98470259157416,14.7063814286827,0.482427379965273,0.523450805993701,PCV20 +Massachusetts.post.PCV7,15F,2969,820000,3,4,0,adjusted_type_specific_negbin,0.00147547990046935,0.000513303168103363,0.00324361997135177,0.395262731662366,0.253462664196128,0.614675280443518,0.000170123300166289,2.02083655214776e-05,0.000864026455062348,3.54240797176599,2.49560124043154,5.15073328448319,4.38069982449349,1.52399710609889,9.63030769494342,0.238286086169655,0.0247130751779754,1.32217529940124,0.380699824493486,0.238286086169655,No PCV +Massachusetts.post.PCV7,16F,2969,820000,3,13,0,adjusted_type_specific_negbin,0.00422374060173487,0.00233177920947765,0.00692662791464886,0.395262731662366,0.253462664196128,0.614675280443518,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,12.5402858465508,6.92305247293913,20.5651582785925,1.61734391963666,0.658519591180363,3.77524890314016,0.45971415344917,1.61734391963666,No PCV +Massachusetts.post.PCV7,17F,2969,820000,3,8,1,adjusted_type_specific_negbin,0.00289435660174243,0.00141191155957583,0.00521216419591942,0.395262731662366,0.253462664196128,0.614675280443518,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,8.59334475057327,4.19196542038065,15.4749154976848,1.07555789214522,0.396836137175541,2.68053610705071,0.593344750573266,0.0755578921452167,PPV23 +Massachusetts.post.PCV7,18B,2969,820000,3,0,2,adjusted_type_specific_negbin,0.000566049336676993,0.000118454084656296,0.00173863006156962,0.395262731662366,0.253462664196128,0.614675280443518,0.00124945709832586,0.000238400207766176,0.00647740004764962,3.54240797176599,2.49560124043154,5.15073328448319,1.68060048059399,0.351690177344542,5.1619926528002,0.677100249934737,0.102145051796076,3.20637789995132,1.68060048059399,1.32289975006526,No PCV +Massachusetts.post.PCV7,18C,2969,820000,3,2,4,adjusted_type_specific_negbin,0.00111484427080275,0.000417578458137052,0.00247778765918464,0.395262731662366,0.253462664196128,0.614675280443518,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,3.30997264001335,1.23979044220891,7.35655156011921,2.94232800039631,1.05744701844633,7.25568972951114,1.30997264001335,1.05767199960369,PCV7 +Massachusetts.post.PCV7,18F,2969,820000,3,1,0,adjusted_type_specific_negbin,0.00043916944089823,5.70380684042207e-05,0.00160623910217355,0.395262731662366,0.253462664196128,0.614675280443518,0.000728671850027043,6.36008620504993e-05,0.00682715327525218,3.54240797176599,2.49560124043154,5.15073328448319,1.30389407002685,0.169346025092131,4.76892389435327,0.297131473533834,0.0178402569433782,2.64381049379548,0.303894070026846,0.297131473533834,No PCV +Massachusetts.post.PCV7,19A,2969,820000,3,113,80,adjusted_type_specific_negbin,0.0387189963632828,0.0322441872671778,0.0460204935424378,0.395262731662366,0.253462664196128,0.614675280443518,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,114.956700202587,95.732991996251,136.634845327498,58.2084094898381,37.7415890779431,91.7175820786467,1.9567002025866,21.7915905101619,PCV13 +Massachusetts.post.PCV7,19F,2969,820000,3,31,2,adjusted_type_specific_negbin,0.010168895713646,0.00703667074040802,0.0141371094200695,0.395262731662366,0.253462664196128,0.614675280443518,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,30.1914513738149,20.8918754282714,41.9730778681862,6.34850954674483,3.53301838428431,11.3314423510879,0.808548626185065,4.34850954674483,PCV7 +Massachusetts.post.PCV7,20,2969,820000,3,0,2,adjusted_type_specific_negbin,0.000660510826720919,0.000148541677584951,0.00186738676360083,0.395262731662366,0.253462664196128,0.614675280443518,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,1.96105664453441,0.441020240749721,5.54427130113087,0.47986608979724,0.0812039975593642,1.990574033028,1.96105664453441,1.52013391020276,PPV23 +Massachusetts.post.PCV7,21,2969,820000,3,7,1,adjusted_type_specific_negbin,0.00271003552940006,0.00129727486183149,0.00495165840941412,0.395262731662366,0.253462664196128,0.614675280443518,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,8.04609548678879,3.85160906477768,14.7014738175505,0.520313219217848,0.180658373277813,1.36565643449342,1.04609548678879,0.479686780782152,No PCV +Massachusetts.post.PCV7,22F,2969,820000,3,26,14,adjusted_type_specific_negbin,0.00941908948616965,0.00646056714201859,0.0131520488460947,0.395262731662366,0.253462664196128,0.614675280443518,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,27.9652766844377,19.1814238446532,39.0484330240552,9.39258721854252,5.15573988543345,17.3490643217612,1.96527668443768,4.60741278145748,PCV15 +Massachusetts.post.PCV7,23A,2969,820000,3,62,1,adjusted_type_specific_negbin,0.0207460126937188,0.0160323427098883,0.0262140846435384,0.395262731662366,0.253462664196128,0.614675280443518,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,61.5949116876511,47.6000255056584,77.8296173066654,3.20012826825401,1.59378627186864,6.25909383153396,0.405088312348866,2.20012826825401,No PCV +Massachusetts.post.PCV7,23B,2969,820000,3,43,6,adjusted_type_specific_negbin,0.0150712129188474,0.0111979802294787,0.0197242020045728,0.395262731662366,0.253462664196128,0.614675280443518,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,44.7464311560579,33.2468033013222,58.5611557515765,3.79771162924399,1.99081733601762,7.16091625398343,1.74643115605789,2.20228837075601,No PCV +Massachusetts.post.PCV7,23F,2969,820000,3,5,2,adjusted_type_specific_negbin,0.00205912999071971,0.000906600038910841,0.00396708745981557,0.395262731662366,0.253462664196128,0.614675280443518,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,6.11355694244681,2.69169551552629,11.7782826681924,1.37592515172345,0.555330741011148,3.07077307586569,1.11355694244681,0.62407484827655,PCV7 +Massachusetts.post.PCV7,25A,2969,820000,3,3,0,adjusted_type_specific_negbin,0.000887530821478335,0.000248004310980167,0.0022782916429267,0.395262731662366,0.253462664196128,0.614675280443518,0.00165141051651395,0.000589976401575755,0.00500660807717493,3.54240797176599,2.49560124043154,5.15073328448319,2.63507900896918,0.736324799300116,6.76424788784937,1.41229594050072,0.329181634035233,5.07145845162233,0.364920991030823,1.41229594050072,No PCV +Massachusetts.post.PCV7,3,2969,820000,3,11,8,adjusted_type_specific_negbin,0.00397856195392666,0.00225252523097954,0.00643851976718493,0.395262731662366,0.253462664196128,0.614675280443518,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,11.8123504412083,6.68774741077825,19.1159651887721,7.822917516616,3.95408483403696,15.2428606932415,0.812350441208261,0.177082483384004,PCV13 +Massachusetts.post.PCV7,31,2969,820000,3,7,0,adjusted_type_specific_negbin,0.00229801074397713,0.00101807208855077,0.00439075750386833,0.395262731662366,0.253462664196128,0.614675280443518,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,6.82279389886811,3.02265603090723,13.0361590289851,1.06982260987093,0.307505402618973,3.27715054794194,0.17720610113189,1.06982260987093,No PCV +Massachusetts.post.PCV7,33A,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000548969311015311,7.97482903329055e-05,0.00184983960504132,0.395262731662366,0.253462664196128,0.614675280443518,1.83168515883687e-05,1.16579300526127e-06,0.000927087809352373,3.54240797176599,2.49560124043154,5.15073328448319,1.62988988440446,0.236772673998397,5.49217378736768,0.0093121781010403,0.000298249480553385,0.513663607424541,0.629889884404459,0.0093121781010403,No PCV +Massachusetts.post.PCV7,33F,2969,820000,3,6,11,adjusted_type_specific_negbin,0.00329563211129044,0.00180563012509071,0.00553079929339239,0.395262731662366,0.253462664196128,0.614675280443518,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,9.78473173842132,5.36091584139433,16.420943102082,4.26450422191618,2.07933708202876,8.59532652224156,3.78473173842132,6.73549577808382,PCV15 +Massachusetts.post.PCV7,34,2969,820000,3,12,0,adjusted_type_specific_negbin,0.00413546123274381,0.00225837463874468,0.00683258221019506,0.395262731662366,0.253462664196128,0.614675280443518,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,12.2781844000164,6.70511430243297,20.2859365820691,0.396203657080662,0.078572016222869,1.42911535992153,0.278184400016384,0.396203657080662,No PCV +Massachusetts.post.PCV7,35B,2969,820000,3,65,0,adjusted_type_specific_negbin,0.0216279797196204,0.0167846491119303,0.0271655673757007,0.395262731662366,0.253462664196128,0.614675280443518,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,64.2134717875531,49.8336232133212,80.6545695384554,2.7403485327957,1.15693588231824,6.05528733013323,0.786528212446882,2.7403485327957,No PCV +Massachusetts.post.PCV7,35F,2969,820000,3,26,1,adjusted_type_specific_negbin,0.00889059310111779,0.00594835497443779,0.0126467464144507,0.395262731662366,0.253462664196128,0.614675280443518,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,26.3961709172187,17.6606659191058,37.5481901045041,1.29713604458411,0.520293152521828,2.96054995814219,0.396170917218722,0.297136044584114,No PCV +Massachusetts.post.PCV7,36,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000536341036649214,7.61390341133726e-05,0.00181550260833393,0.395262731662366,0.253462664196128,0.614675280443518,2.58839998099884e-05,1.1820498282222e-06,0.00170666709060845,3.54240797176599,2.49560124043154,5.15073328448319,1.59239653781152,0.226056792282603,5.39022724414344,0.0127853282910441,0.000308890491953351,0.826739876291953,0.592396537811516,0.0127853282910441,No PCV +Massachusetts.post.PCV7,37,2969,820000,3,3,0,adjusted_type_specific_negbin,0.00119331116461724,0.000352845560422905,0.00282603549773521,0.395262731662366,0.253462664196128,0.614675280443518,8.73857936299313e-05,4.08275642783979e-06,0.000582177503837751,3.54240797176599,2.49560124043154,5.15073328448319,3.54294084774859,1.04759846889561,8.39049939277584,0.0958046389269907,0.00407483733608831,0.742012762548589,0.542940847748594,0.0958046389269907,No PCV +Massachusetts.post.PCV7,38,2969,820000,3,5,2,adjusted_type_specific_negbin,0.00197225517726631,0.000840223812324394,0.00384401894256733,0.395262731662366,0.253462664196128,0.614675280443518,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,5.85562562130369,2.49462449879113,11.4128922404824,1.67324262793065,0.575726393585069,4.3644843495622,0.855625621303687,0.326757372069351,No PCV +Massachusetts.post.PCV7,4,2969,820000,3,0,3,adjusted_type_specific_negbin,0.000677303452120841,0.000184839840384321,0.0017695841114882,0.395262731662366,0.253462664196128,0.614675280443518,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,2.01091394934678,0.54878948610105,5.25389522700847,1.25185472844731,0.334494551458534,3.56019481205298,2.01091394934678,1.74814527155269,PCV7 +Massachusetts.post.PCV7,6A,2969,820000,3,27,12,adjusted_type_specific_negbin,0.0104453168085561,0.00732882801236379,0.0143118998041352,0.395262731662366,0.253462664196128,0.614675280443518,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,31.0121456046029,21.7592903687081,42.4920305184775,4.39555440685152,2.54696082480209,7.57965388981172,4.01214560460294,7.60444559314848,PCV13 +Massachusetts.post.PCV7,6B,2969,820000,3,8,2,adjusted_type_specific_negbin,0.00289634631765988,0.00145563461481602,0.00513896892342834,0.395262731662366,0.253462664196128,0.614675280443518,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,8.59925221713218,4.32177917138876,15.2575987336587,2.10783681805237,0.944718861933415,4.34313127654521,0.599252217132179,0.107836818052375,PCV7 +Massachusetts.post.PCV7,6C,2969,820000,3,65,1,adjusted_type_specific_negbin,0.0219041678134459,0.0171266597721913,0.0275904369648428,0.395262731662366,0.253462664196128,0.614675280443518,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,65.0334742381209,50.8490528636359,81.9160073486182,1.78265304063729,0.703979922537402,4.25891126706545,0.033474238120931,0.782653040637293,No PCV +Massachusetts.post.PCV7,7C,2969,820000,3,5,1,adjusted_type_specific_negbin,0.00196052148598656,0.000803994707398579,0.00391174331777803,0.395262731662366,0.253462664196128,0.614675280443518,0.000395968078807268,0.000112206548547661,0.00124464123083086,3.54240797176599,2.49560124043154,5.15073328448319,5.82078829189411,2.38706028626638,11.613965910483,0.741895540174792,0.176205178148825,2.61101124774878,0.820788291894108,0.258104459825208,No PCV +Massachusetts.post.PCV7,7F,2969,820000,3,21,28,adjusted_type_specific_negbin,0.00670846606666675,0.00423196970135175,0.0100250693469952,0.395262731662366,0.253462664196128,0.614675280443518,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,19.9174357519336,12.5647180433134,29.7644308912287,61.79548795945,31.896128319975,123.645429741302,1.08256424806641,33.79548795945,PCV10 +Massachusetts.post.PCV7,9A,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000482652676117893,6.50539345287221e-05,0.00168196202917093,0.395262731662366,0.253462664196128,0.614675280443518,0.000335225096715175,1.03750856015762e-05,0.00445225735285593,3.54240797176599,2.49560124043154,5.15073328448319,1.43299579539402,0.193145131615776,4.99374526460848,0.14826899334379,0.00389043891524559,1.84608215259401,0.432995795394025,0.14826899334379,No PCV +Massachusetts.post.PCV7,9N,2969,820000,3,4,0,adjusted_type_specific_negbin,0.00137128960491745,0.000480963296942769,0.00305656679825015,0.395262731662366,0.253462664196128,0.614675280443518,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,4.07135883699991,1.42798002862308,9.07494682400469,0.694841716232345,0.191264415046763,2.11620379467382,0.0713588369999094,0.694841716232345,PPV23 +Massachusetts.post.PCV7,9V,2969,820000,3,2,0,adjusted_type_specific_negbin,0.000608587875912481,0.000136139377622899,0.00177392210751208,0.395262731662366,0.253462664196128,0.614675280443518,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,1.80689740358416,0.404197812162388,5.26677473720335,1.21335379822727,0.261618841153395,3.92138333881373,0.193102596415845,1.21335379822727,PCV7 +Navajo.post.PCV7,1,6541,65048,6,8,22,adjusted_type_specific_negbin,0.00171966888518857,0.000987698561773841,0.0027985922966354,1,1,1,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,11.2483541780184,6.4605362925627,18.3055922122921,11.551674034837,6.11249133375942,22.2284449659835,3.24835417801841,10.448325965163,PCV10 +Navajo.post.PCV7,10A,6541,65048,6,85,0,adjusted_type_specific_negbin,0.0128300889277119,0.0102918305650182,0.0157386011925905,1,1,1,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,83.9216116761638,67.3188637257839,102.946190400735,3.61256658338596,1.94747271331814,6.66179316548035,1.07838832383618,3.61256658338596,PCV20 +Navajo.post.PCV7,10C,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000240762148105704,3.27056057746807e-05,0.000814359934988871,1,1,1,8.49579951853475e-05,1.27857906584461e-06,0.0213258979431922,3.54240797176599,2.49560124043154,5.15073328448319,1.57482521075941,0.213927367372186,5.3267283347622,0.00777127252206179,7.33306142328084e-05,1.39415280909062,0.574825210759412,0.00777127252206179,No PCV +Navajo.post.PCV7,10F,6541,65048,6,25,0,adjusted_type_specific_negbin,0.0038983052780134,0.00259580056791616,0.00559456177728902,1,1,1,2.13046068505099e-05,1.16050548851916e-06,0.00113955139125871,3.54240797176599,2.49560124043154,5.15073328448319,25.4988148234857,16.9791315147396,36.5940285852475,0.0326146410229414,0.0017078130530414,1.70850943809883,0.498814823485652,0.0326146410229414,No PCV +Navajo.post.PCV7,11A,6541,65048,6,92,0,adjusted_type_specific_negbin,0.0141262984964889,0.011439418405578,0.0171930168156022,1,1,1,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,92.4001184655336,74.8252357908858,112.459522990854,0.372890810633119,0.165415113936007,0.775986885479068,0.400118465533581,0.372890810633119,PCV20 +Navajo.post.PCV7,12F,6541,65048,6,25,15,adjusted_type_specific_negbin,0.00415393620917341,0.00281736680631173,0.00583133322117795,1,1,1,0.00604185287379925,0.00279991943562254,0.0141061491643519,3.54240797176599,2.49560124043154,5.15073328448319,27.1708967442033,18.428396280085,38.142750599725,9.72746969417084,4.50789479435976,22.6893107674133,2.17089674420329,5.27253030582916,PCV20 +Navajo.post.PCV7,14,6541,65048,6,4,0,adjusted_type_specific_negbin,0.000599525840549529,0.000204978559062859,0.00133763335026234,1,1,1,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,3.92149852303447,1.34076475483016,8.74945974406599,0.988115031991955,0.313099275434756,2.48534999553001,0.0785014769655294,0.988115031991955,PCV7 +Navajo.post.PCV7,15A,6541,65048,6,132,4,adjusted_type_specific_negbin,0.0203401960875236,0.0170661799441747,0.0240456473882644,1,1,1,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,133.045222608492,111.629883014847,157.282579566637,3.31881618878003,1.7102291732672,6.43825959903454,1.0452226084922,0.681183811219971,No PCV +Navajo.post.PCV7,15B/C,6541,65048,6,124,2,adjusted_type_specific_negbin,0.0189899417083213,0.015868603352104,0.0224728147690127,1,1,1,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,124.21320871413,103.796534526112,146.994681404112,2.59200208860845,1.49734269625365,4.48549577754228,0.213208714129607,0.592002088608447,PCV20 +Navajo.post.PCV7,16F,6541,65048,6,83,1,adjusted_type_specific_negbin,0.0126865577329405,0.0101876792644531,0.0155505972429802,1,1,1,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,82.9827741311636,66.6376100687877,101.716456566333,1.96301947483623,0.923717452122295,4.03270116040463,0.0172258688364053,0.963019474836235,No PCV +Navajo.post.PCV7,17F,6541,65048,6,96,1,adjusted_type_specific_negbin,0.0146565252157809,0.011940449946493,0.0177308313353024,1,1,1,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,95.8683314364227,78.1024831000105,115.977367764213,2.19649183034913,0.999409579148742,4.75622786285507,0.131668563577335,1.19649183034913,PPV23 +Navajo.post.PCV7,18C,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000223466866824515,3.21176897372871e-05,0.000742029194606802,1,1,1,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,1.46169677589915,0.210081808571595,4.85361296192309,0.236948655385422,0.0328181922205191,0.905959754690293,0.461696775899151,0.236948655385422,PCV7 +Navajo.post.PCV7,19A,6541,65048,6,208,29,adjusted_type_specific_negbin,0.0321182890820855,0.0280172394437726,0.0366213679352463,1,1,1,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,210.085728885922,183.260763201717,239.540367664446,19.4794024498533,12.4314863296432,30.6316375002152,2.08572888592153,9.5205975501467,PCV13 +Navajo.post.PCV7,19F,6541,65048,6,35,1,adjusted_type_specific_negbin,0.00540847741093789,0.00383967946032239,0.00736750289766495,1,1,1,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,35.3768507449448,25.1153433499688,48.1908364536264,1.36091478434634,0.743860622577017,2.45215788893516,0.376850744944768,0.360914784346342,PCV7 +Navajo.post.PCV7,20,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000243481489413719,3.20555806475524e-05,0.000811845912940656,1,1,1,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,1.59261242225514,0.20967555301564,5.31028411654483,0.0703601622396604,0.00692530045717932,0.39632365912981,0.592612422255138,0.0703601622396604,PPV23 +Navajo.post.PCV7,21,6541,65048,6,88,2,adjusted_type_specific_negbin,0.013656839677017,0.0110772184863254,0.016635141005933,1,1,1,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,89.3293883273684,72.4560861190547,108.810457319808,1.07202633450904,0.453734415890452,2.37515424547377,1.32938832736842,0.927973665490959,No PCV +Navajo.post.PCV7,22A,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000238565778220385,3.19953010932295e-05,0.000821686611881646,1,1,1,8.59162706765511e-05,1.25009532348606e-06,0.0209610130029039,3.54240797176599,2.49560124043154,5.15073328448319,1.56045875533954,0.209281264450814,5.37465212831785,0.00763826480891884,7.1188143655495e-05,1.3684072721291,0.560458755339535,0.00763826480891884,No PCV +Navajo.post.PCV7,22F,6541,65048,6,134,4,adjusted_type_specific_negbin,0.020397320324594,0.017164211139565,0.024012364035703,1,1,1,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,133.418872243169,112.271105063895,157.064873157533,8.18009722258332,4.54346091959609,15.105542646507,0.581127756830767,4.18009722258332,PCV15 +Navajo.post.PCV7,23A,6541,65048,6,89,1,adjusted_type_specific_negbin,0.0137164274546833,0.0111139252266194,0.0167485573326781,1,1,1,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,89.7191519810833,72.6961849073176,109.552313513047,0.852125592060584,0.416949004580391,1.70634252022159,0.719151981083257,0.147874407939416,No PCV +Navajo.post.PCV7,23B,6541,65048,6,137,3,adjusted_type_specific_negbin,0.0211289201662912,0.0178213135041078,0.0247992993066026,1,1,1,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,138.204266807711,116.569211630369,162.212216764488,2.14144240946893,1.10795032775326,4.04805882857443,1.20426680771061,0.858557590531066,No PCV +Navajo.post.PCV7,27,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000199998045183226,2.80230921582756e-05,0.000709372413987031,1,1,1,0.00450929445931807,0.00105355976436417,0.0191759279052972,3.54240797176599,2.49560124043154,5.15073328448319,1.30818721354348,0.183299045807281,4.64000495988917,0.345869807280063,0.0353020439451124,1.96084726553638,0.308187213543481,0.345869807280063,No PCV +Navajo.post.PCV7,3,6541,65048,6,73,10,adjusted_type_specific_negbin,0.0113153262974622,0.00900474768872598,0.0139789138105404,1,1,1,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,74.0135493117004,58.9000546319567,91.4360752347448,8.98953694791,5.25532296738283,15.5768127645888,1.01354931170042,1.01046305209,PCV13 +Navajo.post.PCV7,31,6541,65048,6,50,1,adjusted_type_specific_negbin,0.00768458148922545,0.00576109098256543,0.0100333727017115,1,1,1,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,50.2648475210237,37.6832961169605,65.6282908418946,1.46049751963243,0.497602258338093,3.84257493486574,0.264847521023668,0.460497519632428,No PCV +Navajo.post.PCV7,33A,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000255035599511876,3.76126666933241e-05,0.000843422046494801,1,1,1,1.83168515883687e-05,1.16579300526127e-06,0.000927087809352373,3.54240797176599,2.49560124043154,5.15073328448319,1.66818785640718,0.246024452841033,5.51682360612249,0.00168820533960234,5.56095995754122e-05,0.106261771861995,0.668187856407183,0.00168820533960234,No PCV +Navajo.post.PCV7,33F,6541,65048,6,60,2,adjusted_type_specific_negbin,0.00909757897345868,0.00697812908954425,0.0115578854150733,1,1,1,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,59.5072640653933,45.643942374709,75.6001284999942,4.7591772084206,2.39060078099725,9.46974502193091,0.492735934606742,2.7591772084206,PCV15 +Navajo.post.PCV7,34,6541,65048,6,89,1,adjusted_type_specific_negbin,0.0137675693389595,0.011093854386357,0.0167908459464433,1,1,1,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,90.0536710461339,72.564901541161,109.828923335686,0.538492651281566,0.113145086441442,1.75906128427691,1.05367104613387,0.461507348718434,No PCV +Navajo.post.PCV7,35A,6541,65048,6,55,0,adjusted_type_specific_negbin,0.00848882418958793,0.00646782992065231,0.0109000658842374,1,1,1,1.46446185008473e-05,1.12973321747656e-06,0.000569025070445038,3.54240797176599,2.49560124043154,5.15073328448319,55.5253990240946,42.3060755109868,71.297330948797,0.0485432341783624,0.0036990984977486,1.8663937576898,0.525399024094625,0.0485432341783624,No PCV +Navajo.post.PCV7,35B,6541,65048,6,137,2,adjusted_type_specific_negbin,0.0211501793711408,0.0179059265587967,0.0247571461853935,1,1,1,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,138.343323266632,117.122665621089,161.936493198659,1.07657489163554,0.458066445777213,2.35431307086037,1.34332326663184,0.923425108364464,No PCV +Navajo.post.PCV7,35F,6541,65048,6,58,0,adjusted_type_specific_negbin,0.00888465660795865,0.00682549846187058,0.0113505576315224,1,1,1,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,58.1145388726576,44.6455854390955,74.2439974677879,0.522969902688725,0.214210804963893,1.1765718011905,0.114538872657555,0.522969902688725,No PCV +Navajo.post.PCV7,37,6541,65048,6,10,0,adjusted_type_specific_negbin,0.00161655663132199,0.000821884134250562,0.00278190927130103,1,1,1,8.73857936299313e-05,4.08275642783979e-06,0.000582177503837751,3.54240797176599,2.49560124043154,5.15073328448319,10.5738969254771,5.37594412213293,18.19646854358,0.0538209781779483,0.00246152963411748,0.38421624247051,0.573896925477143,0.0538209781779483,No PCV +Navajo.post.PCV7,38,6541,65048,6,32,1,adjusted_type_specific_negbin,0.00491872162213918,0.00344290415492204,0.00679978934059146,1,1,1,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,32.1733581304124,22.520036077345,44.4774220768088,1.69400201492634,0.685517809129915,3.98539612089419,0.173358130412403,0.694002014926341,No PCV +Navajo.post.PCV7,4,6541,65048,6,5,0,adjusted_type_specific_negbin,0.000786937747208919,0.000305476516737939,0.00162094256337274,1,1,1,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,5.14735980449354,1.99812189598286,10.6025853070211,0.583157418748032,0.195029693567748,1.54787686273398,0.147359804493538,0.583157418748032,PCV7 +Navajo.post.PCV7,5,6541,65048,6,2,0,adjusted_type_specific_negbin,0.000301738987451936,6.81961403412155e-05,0.000852710564433448,1,1,1,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,1.97367471692311,0.44607095397189,5.57757980195919,0.857509679973798,0.166861918604215,3.12476756500839,0.0263252830768894,0.857509679973798,PCV10 +Navajo.post.PCV7,6B,6541,65048,6,4,0,adjusted_type_specific_negbin,0.000682702205249152,0.00023177364010699,0.00151670346795365,1,1,1,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,4.4655551245347,1.51603137993982,9.92075738388486,0.199506138168152,0.0604624373653286,0.5150451748325,0.4655551245347,0.199506138168152,PCV7 +Navajo.post.PCV7,7C,6541,65048,6,60,1,adjusted_type_specific_negbin,0.00922744468507965,0.00708905821197032,0.0117561183315655,1,1,1,0.000395968078807268,0.000112206548547661,0.00124464123083086,3.54240797176599,2.49560124043154,5.15073328448319,60.356715685106,46.3695297644979,76.8967700067697,1.4294318525215,0.394192506077097,4.49292763179067,0.35671568510601,0.429431852521502,No PCV +Navajo.post.PCV7,7F,6541,65048,6,13,24,adjusted_type_specific_negbin,0.00268095114149035,0.00170614677129398,0.00399931547888777,1,1,1,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,17.5361014164883,11.1599060310339,26.1595225474049,9.91975830412319,5.55124123957543,18.0372299035269,4.53610141648835,14.0802416958768,PCV10 +Navajo.post.PCV7,8,6541,65048,6,11,1,adjusted_type_specific_negbin,0.00174619211235642,0.000942368295103223,0.00292296119791896,1,1,1,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,11.4218426069234,6.16403101827018,19.1190891955879,1.30154616221787,0.508990906211123,3.14198397265686,0.421842606923359,0.301546162217873,PCV20 +Navajo.post.PCV7,9N,6541,65048,6,9,0,adjusted_type_specific_negbin,0.0014354632448385,0.000717157848016676,0.00253455944426197,1,1,1,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,9.38936508448862,4.69092948387708,16.5785533249175,0.291923866037245,0.0994005217874217,0.80453235727837,0.389365084488624,0.291923866037245,PPV23 +Navajo.post.PCV7,9V,6541,65048,6,7,0,adjusted_type_specific_negbin,0.00106241979429316,0.000473042622759386,0.00201511314643805,1,1,1,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,6.94928787447159,3.09417179546914,13.1808550908513,0.848573794946365,0.318924976913644,2.07785327352837,0.050712125528408,0.848573794946365,PCV7 +Netherlands.post.PCV10,1,659,222671,4,3,3,adjusted_type_specific_negbin,0.00334734555001978,0.00103874542983135,0.00881468599933743,0.168032907050554,0.0976137212211191,0.288789135906522,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,2.20590071746304,0.684533238258859,5.80887807356336,8.5455368818631,2.6431821257961,25.6026447717251,0.794099282536962,5.5455368818631,PCV10 +Netherlands.post.PCV10,10A,659,222671,4,13,4,adjusted_type_specific_negbin,0.022177788091214,0.0131027205196629,0.0345819374181112,0.168032907050554,0.0976137212211191,0.288789135906522,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,14.61516235211,8.63469282245784,22.7894967585353,2.38043835408019,1.12447407715219,4.9395286772068,1.61516235211,1.61956164591981,PCV20 +Netherlands.post.PCV10,10B,659,222671,4,2,1,adjusted_type_specific_negbin,0.00479305384502613,0.00135986324787563,0.011768702962632,0.168032907050554,0.0976137212211191,0.288789135906522,0.000509389844494032,8.66360486448286e-05,0.00249463469166522,3.54240797176599,2.49560124043154,5.15073328448319,3.15862248387222,0.896149880350043,7.75557525237449,0.356121392116147,0.0476154773602877,1.92855727107443,1.15862248387222,0.643878607883853,No PCV +Netherlands.post.PCV10,11A,659,222671,4,31,0,adjusted_type_specific_negbin,0.0472880618732501,0.0328199922887999,0.0652893897378763,0.168032907050554,0.0976137212211191,0.288789135906522,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,31.1628327744718,21.6283749183191,43.0257078372605,0.476113035062322,0.194676715185437,1.09555264239864,0.162832774471809,0.476113035062322,PCV20 +Netherlands.post.PCV10,14,659,222671,4,0,1,adjusted_type_specific_negbin,0.00130771049031211,0.00018372285646396,0.00475985440743608,0.168032907050554,0.0976137212211191,0.288789135906522,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,0.86178121311568,0.121073362409749,3.13674405450038,0.822669954154982,0.117134228939449,3.11208316992784,0.86178121311568,0.177330045845018,PCV7 +Netherlands.post.PCV10,15A,659,222671,4,8,0,adjusted_type_specific_negbin,0.012196364554917,0.00577083530558803,0.0220624978305725,0.168032907050554,0.0976137212211191,0.288789135906522,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,8.03740424169031,3.80298046638251,14.5391860703473,0.756113275383058,0.278856591275857,1.87717577454181,0.0374042416903109,0.756113275383058,No PCV +Netherlands.post.PCV10,15B/C,659,222671,4,28,2,adjusted_type_specific_negbin,0.0432128780786091,0.0298312282460353,0.0601177924893268,0.168032907050554,0.0976137212211191,0.288789135906522,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,28.4772866538034,19.6587794141372,39.6176252504663,2.25046014908664,1.15169843620113,4.38105649262625,0.477286653803425,0.25046014908664,PCV20 +Netherlands.post.PCV10,15F,659,222671,4,1,0,adjusted_type_specific_negbin,0.00242183469388111,0.000350517137110802,0.00797974822490754,0.168032907050554,0.0976137212211191,0.288789135906522,0.000170123300166289,2.02083655214776e-05,0.000864026455062348,3.54240797176599,2.49560124043154,5.15073328448319,1.59598906326765,0.230990793356019,5.25865408021407,0.0565780334854059,0.00385656202588938,0.44562371261873,0.595989063267653,0.0565780334854059,No PCV +Netherlands.post.PCV10,16F,659,222671,4,10,1,adjusted_type_specific_negbin,0.0161731876527415,0.00847092507158091,0.0275327866403689,0.168032907050554,0.0976137212211191,0.288789135906522,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,10.6581306631567,5.58233962217182,18.1441063960031,0.950373907223166,0.36612015463473,2.32837560626997,0.658130663156655,0.0496260927768344,No PCV +Netherlands.post.PCV10,17F,659,222671,4,6,1,adjusted_type_specific_negbin,0.0106193082196574,0.00485085422339433,0.0199460838869888,0.168032907050554,0.0976137212211191,0.288789135906522,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,6.99812411675424,3.19671293321686,13.1444692815256,0.604166615174247,0.205197617660865,1.61820763589342,0.998124116754241,0.395833384825753,PPV23 +Netherlands.post.PCV10,18C,659,222671,4,0,1,adjusted_type_specific_negbin,0.00153427206807873,0.000210255135051826,0.00545994759678192,0.168032907050554,0.0976137212211191,0.288789135906522,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,1.01108529286388,0.138558133999153,3.59810546627929,0.622529791682453,0.0814998666474554,2.43453680006167,1.01108529286388,0.377470208317547,PCV7 +Netherlands.post.PCV10,19A,659,222671,4,41,5,adjusted_type_specific_negbin,0.0606484756888401,0.0443510367552146,0.0800786653419951,0.168032907050554,0.0976137212211191,0.288789135906522,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,39.9673454789456,29.2273332216864,52.7718404603748,14.0115885018028,7.71393801068059,25.5734668889693,1.0326545210544,9.01158850180278,PCV13 +Netherlands.post.PCV10,19F,659,222671,4,5,1,adjusted_type_specific_negbin,0.00877403377077112,0.00363784382187516,0.0174290050737712,0.168032907050554,0.0976137212211191,0.288789135906522,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,5.78208825493817,2.39733907861573,11.4857143436152,0.840128112978302,0.304995529514168,2.01660151467778,0.782088254938168,0.159871887021698,PCV7 +Netherlands.post.PCV10,21,659,222671,4,14,0,adjusted_type_specific_negbin,0.0214018506492494,0.0122649471795803,0.0340424252761192,0.168032907050554,0.0976137212211191,0.288789135906522,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,14.1038195778554,8.08260019134344,22.4339582569626,0.633592935770696,0.229470154901545,1.62307508104783,0.103819577855386,0.633592935770696,No PCV +Netherlands.post.PCV10,22F,659,222671,4,5,2,adjusted_type_specific_negbin,0.0092136644442573,0.00407470614379204,0.0176978801918241,0.168032907050554,0.0976137212211191,0.288789135906522,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,6.07180486876556,2.68523134875895,11.6629030464121,1.4072662819808,0.537063320023301,3.37650089650926,1.07180486876556,0.5927337180192,PCV15 +Netherlands.post.PCV10,23A,659,222671,4,18,1,adjusted_type_specific_negbin,0.028656760144688,0.0180199624080512,0.0426830373328054,0.168032907050554,0.0976137212211191,0.288789135906522,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,18.8848049353494,11.8751552269057,28.1281216023188,0.67997919239569,0.290745960694985,1.51032528873455,0.884804935349365,0.32002080760431,No PCV +Netherlands.post.PCV10,23B,659,222671,4,45,3,adjusted_type_specific_negbin,0.0693611456672145,0.0521062439626048,0.090133116063298,0.168032907050554,0.0976137212211191,0.288789135906522,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,45.7089949946944,34.3380147713566,59.3977234857134,2.67636492216733,1.31478192517801,5.45287667343707,0.708994994694393,0.323635077832666,No PCV +Netherlands.post.PCV10,23F,659,222671,4,0,1,adjusted_type_specific_negbin,0.00212528064406327,0.000307910135153104,0.00711896431298979,0.168032907050554,0.0976137212211191,0.288789135906522,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,1.40055994443769,0.202912779065896,4.69139748226027,0.218603719458718,0.0307752265055096,0.828272174308723,1.40055994443769,0.781396280541282,PCV7 +Netherlands.post.PCV10,24F,659,222671,4,5,2,adjusted_type_specific_negbin,0.0080668783237884,0.00337900157791752,0.0160976407001572,0.168032907050554,0.0976137212211191,0.288789135906522,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,5.31607281537656,2.22676203984765,10.6083452214036,2.63375499368078,0.956801931267636,6.94518288869112,0.316072815376558,0.633754993680781,No PCV +Netherlands.post.PCV10,27,659,222671,4,0,2,adjusted_type_specific_negbin,0.00185296230828362,0.000336943291175817,0.00630113972797158,0.168032907050554,0.0976137212211191,0.288789135906522,0.00450929445931807,0.00105355976436417,0.0191759279052972,3.54240797176599,2.49560124043154,5.15073328448319,1.2211021611589,0.222045628884863,4.15245108073327,1.21972607165813,0.217192831636433,5.10272114420825,1.2211021611589,0.780273928341866,No PCV +Netherlands.post.PCV10,3,659,222671,4,2,5,adjusted_type_specific_negbin,0.00688756386916465,0.00287272551445132,0.0139163716286182,0.168032907050554,0.0976137212211191,0.288789135906522,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,4.5389045897795,1.89312611402342,9.17088890325939,2.09079195085752,0.827351945632697,4.74447484995226,2.5389045897795,2.90920804914248,PCV13 +Netherlands.post.PCV10,31,659,222671,4,2,0,adjusted_type_specific_negbin,0.00369319466026934,0.000864611597964988,0.00993305277492922,0.168032907050554,0.0976137212211191,0.288789135906522,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,2.43381528111749,0.569779043058927,6.54588177867836,0.259920528210638,0.0469534158418601,1.03418223137437,0.433815281117494,0.259920528210638,No PCV +Netherlands.post.PCV10,33A,659,222671,4,1,0,adjusted_type_specific_negbin,0.00248139725117664,0.000360926128878747,0.00824130345312043,0.168032907050554,0.0976137212211191,0.288789135906522,1.83168515883687e-05,1.16579300526127e-06,0.000927087809352373,3.54240797176599,2.49560124043154,5.15073328448319,1.6352407885254,0.237850318931094,5.43101897560637,0.00647939238849039,0.000194850852496664,0.356402429449209,0.635240788525404,0.00647939238849039,No PCV +Netherlands.post.PCV10,33F,659,222671,4,7,2,adjusted_type_specific_negbin,0.0113677659706912,0.00541121204259058,0.0209499123226602,0.168032907050554,0.0976137212211191,0.288789135906522,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,7.49135777468548,3.56598873606719,13.8059922206331,2.26029451137225,0.8982799639318,5.45737573474174,0.491357774685481,0.260294511372253,PCV15 +Netherlands.post.PCV10,34,659,222671,4,0,1,adjusted_type_specific_negbin,0.0024570135649513,0.000368004812953329,0.00804627991993603,0.168032907050554,0.0976137212211191,0.288789135906522,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,1.61917193930291,0.242515171736244,5.30249846723784,0.034746463571198,0.00324759213153123,0.205555437707881,1.61917193930291,0.965253536428802,No PCV +Netherlands.post.PCV10,35B,659,222671,4,12,0,adjusted_type_specific_negbin,0.0187244735369597,0.0101565907824727,0.0308295604245754,0.168032907050554,0.0976137212211191,0.288789135906522,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,12.3394280608565,6.6931933256495,20.3166803197952,0.36140104749556,0.126713368679908,0.959131671530499,0.339428060856459,0.36140104749556,No PCV +Netherlands.post.PCV10,35F,659,222671,4,12,0,adjusted_type_specific_negbin,0.0186688556907668,0.0101926359563468,0.0307087027168646,0.168032907050554,0.0976137212211191,0.288789135906522,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,12.3027759002153,6.71694709523251,20.2370350904138,0.415128255425504,0.147395651213348,1.07668807692637,0.302775900215298,0.415128255425504,No PCV +Netherlands.post.PCV10,37,659,222671,4,1,0,adjusted_type_specific_negbin,0.00246738364927603,0.000364774655398762,0.00819873979727533,0.168032907050554,0.0976137212211191,0.288789135906522,8.73857936299313e-05,4.08275642783979e-06,0.000582177503837751,3.54240797176599,2.49560124043154,5.15073328448319,1.6260058248729,0.240386497907784,5.40296952640444,0.028956019249606,0.000944291866539499,0.299228615991428,0.626005824872903,0.028956019249606,No PCV +Netherlands.post.PCV10,38,659,222671,4,4,0,adjusted_type_specific_negbin,0.00607241924565459,0.00205436604835867,0.013615139533051,0.168032907050554,0.0976137212211191,0.288789135906522,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,4.00172428288638,1.35382722586836,8.97237695228062,0.787499426579892,0.208468796256009,2.46058335578016,0.00172428288637771,0.787499426579892,No PCV +Netherlands.post.PCV10,4,659,222671,4,0,1,adjusted_type_specific_negbin,0.00170960788562695,0.000232285485571331,0.00598803895955336,0.168032907050554,0.0976137212211191,0.288789135906522,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,1.12663159662816,0.153076134991507,3.94611767434566,0.487457628271538,0.0648298647401917,1.91902697616425,1.12663159662816,0.512542371728462,PCV7 +Netherlands.post.PCV10,6A,659,222671,4,2,0,adjusted_type_specific_negbin,0.00367474618555717,0.000868363952602786,0.0101047738850392,0.168032907050554,0.0976137212211191,0.288789135906522,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,2.42165773628217,0.572251844765236,6.65904599024083,0.236916879530266,0.0519826646135862,0.761720787143262,0.421657736282174,0.236916879530266,PCV13 +Netherlands.post.PCV10,6C,659,222671,4,44,2,adjusted_type_specific_negbin,0.0689749265461561,0.0514191731420854,0.0895570030773883,0.168032907050554,0.0976137212211191,0.288789135906522,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,45.4544765939169,33.8852351006343,59.0180650279989,0.861463586286353,0.327325699288821,2.12315542082796,1.45447659391686,1.13853641371365,No PCV +Netherlands.post.PCV10,7F,659,222671,4,3,2,adjusted_type_specific_negbin,0.00376875305449955,0.00121010106021832,0.00938220782353878,0.168032907050554,0.0976137212211191,0.288789135906522,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,2.4836082629152,0.797456598683872,6.18287495571206,5.30910482795009,1.66917464128793,15.1684540503923,0.516391737084797,3.30910482795009,PCV10 +Netherlands.post.PCV10,8,659,222671,4,0,2,adjusted_type_specific_negbin,0.00257394459369087,0.000564518305241536,0.00773469718527281,0.168032907050554,0.0976137212211191,0.288789135906522,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,1.69622948724229,0.372017563154173,5.09716544509478,0.731388107012732,0.150852182328039,2.50084715588,1.69622948724229,1.26861189298727,PCV20 +Netherlands.post.PCV10,9N,659,222671,4,3,0,adjusted_type_specific_negbin,0.0049599725074926,0.00147006306452665,0.0120672368513748,0.168032907050554,0.0976137212211191,0.288789135906522,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,3.26862188243762,0.96877155952306,7.952309085056,0.387887637418728,0.089277751429316,1.30883897978261,0.268621882437625,0.387887637418728,PPV23 +Netherlands.post.PCV10,9V,659,222671,4,0,1,adjusted_type_specific_negbin,0.00168362379705587,0.000223693105331857,0.00591842228859336,0.168032907050554,0.0976137212211191,0.288789135906522,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,1.10950808225982,0.147413756413694,3.90024028818303,0.514999244706689,0.0675647009986176,1.99579471452866,1.10950808225982,0.485000755293311,PCV7 +Netherlands.post.PCV7,1,660,232251,4,2,9,adjusted_type_specific_negbin,0.00411583831896839,0.00155743242585411,0.00944526978561722,0.147371614866085,0.0890058782232559,0.243896039032642,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,2.71645329051914,1.02790540106372,6.23387805850737,9.59142681333365,3.79323586156119,24.2341635692583,0.71645329051914,0.591426813333648,PCV10 +Netherlands.post.PCV7,10A,660,232251,4,20,8,adjusted_type_specific_negbin,0.0347184057184131,0.0228350527691199,0.0499224903447683,0.147371614866085,0.0890058782232559,0.243896039032642,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,22.9141477741527,15.0711348276191,32.9488436275471,3.41235449443772,1.75810057390285,6.52879740576092,2.91414777415266,4.58764550556228,PCV20 +Netherlands.post.PCV7,11A,660,232251,4,36,0,adjusted_type_specific_negbin,0.0548786355657033,0.039408655623875,0.0735193431359182,0.147371614866085,0.0890058782232559,0.243896039032642,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,36.2198994733642,26.0097127117575,48.522766469706,0.505725732742675,0.212175227457508,1.12098916517534,0.219899473364165,0.505725732742675,PCV20 +Netherlands.post.PCV7,12F,660,232251,4,1,0,adjusted_type_specific_negbin,0.00132786538243989,0.000187136637173847,0.0050357662230117,0.147371614866085,0.0890058782232559,0.243896039032642,0.00604185287379925,0.00279991943562254,0.0141061491643519,3.54240797176599,2.49560124043154,5.15073328448319,0.876391152410326,0.123510180534739,3.32360570718772,1.08668718829872,0.150000615364165,4.72880038134201,0.123608847589674,1.08668718829872,PCV20 +Netherlands.post.PCV7,14,660,232251,4,2,0,adjusted_type_specific_negbin,0.00255185699975829,0.000540603155845189,0.00764622387340832,0.147371614866085,0.0890058782232559,0.243896039032642,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,1.68422561984047,0.356798082857825,5.04650775644949,1.46865105722938,0.31102651701627,4.75919052638761,0.31577438015953,1.46865105722938,PCV7 +Netherlands.post.PCV7,15A,660,232251,4,2,2,adjusted_type_specific_negbin,0.00625687360760516,0.002188374129981,0.013643167799629,0.147371614866085,0.0890058782232559,0.243896039032642,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,4.1295365810194,1.44432692578746,9.00449074775512,0.354405051341275,0.107768057731846,0.974910050504725,2.1295365810194,1.64559494865872,No PCV +Netherlands.post.PCV7,15B/C,660,232251,4,29,2,adjusted_type_specific_negbin,0.0447102913464312,0.0309866488984402,0.0617980015852649,0.147371614866085,0.0890058782232559,0.243896039032642,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,29.5087922886446,20.4511882729705,40.7866810462749,2.13851390721273,1.12767802099848,4.02479707006299,0.508792288644571,0.138513907212732,PCV20 +Netherlands.post.PCV7,16F,660,232251,4,12,3,adjusted_type_specific_negbin,0.0212169317547051,0.012394609119278,0.033398419639499,0.147371614866085,0.0890058782232559,0.243896039032642,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,14.0031749581054,8.18044201872348,22.0429569620694,1.14587486729609,0.474594623768018,2.5916451742616,2.00317495810538,1.85412513270391,No PCV +Netherlands.post.PCV7,17F,660,232251,4,9,2,adjusted_type_specific_negbin,0.0159460654091603,0.00841513896777783,0.0270375970117051,0.147371614866085,0.0890058782232559,0.243896039032642,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,10.5244031700458,5.55399171873337,17.8448140277253,0.833050129802505,0.316896637692904,2.06474657304623,1.52440317004581,1.1669498701975,PPV23 +Netherlands.post.PCV7,18C,660,232251,4,2,2,adjusted_type_specific_negbin,0.00443832571851275,0.00147409820230375,0.0104262972279169,0.147371614866085,0.0890058782232559,0.243896039032642,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,2.92929497421842,0.972904813520477,6.88135617042513,1.64616654389917,0.513884843019878,4.38711738133205,0.929294974218417,0.35383345610083,PCV7 +Netherlands.post.PCV7,19A,660,232251,4,68,10,adjusted_type_specific_negbin,0.101633882958137,0.0798361310176936,0.126470201876456,0.147371614866085,0.0890058782232559,0.243896039032642,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,67.0783627523706,52.6918464716777,83.4703332384607,21.5479171541341,12.607451644817,36.7861528912416,0.921637247629434,11.5479171541341,PCV13 +Netherlands.post.PCV7,19F,660,232251,4,8,1,adjusted_type_specific_negbin,0.0129022381098302,0.0063585546949955,0.0230225574828453,0.147371614866085,0.0890058782232559,0.243896039032642,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,8.51547715248796,4.19664609869703,15.1948879386779,1.13439256617564,0.484313982693086,2.45846096431128,0.515477152487957,0.134392566175642,PCV7 +Netherlands.post.PCV7,21,660,232251,4,16,0,adjusted_type_specific_negbin,0.0242942033046206,0.0146393313191785,0.0376451186684984,0.147371614866085,0.0890058782232559,0.243896039032642,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,16.0341741810496,9.66195867065779,24.845778321209,0.664428181829692,0.246586499257443,1.6459065677288,0.0341741810495968,0.664428181829692,No PCV +Netherlands.post.PCV7,22F,660,232251,4,7,4,adjusted_type_specific_negbin,0.0136388385981685,0.00705671262271327,0.0235436582211121,0.147371614866085,0.0890058782232559,0.243896039032642,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,9.00163347479121,4.65743033099075,15.538814425934,1.90795532685239,0.840058609544706,4.16180666477022,2.00163347479121,2.09204467314761,PCV15 +Netherlands.post.PCV7,23A,660,232251,4,11,0,adjusted_type_specific_negbin,0.0171814717110356,0.00909145517431172,0.0290903902895018,0.147371614866085,0.0890058782232559,0.243896039032642,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,11.3397713292835,6.00036041504574,19.1996575910712,0.370158901391028,0.146761601295924,0.886824018210576,0.339771329283518,0.370158901391028,No PCV +Netherlands.post.PCV7,23B,660,232251,4,24,1,adjusted_type_specific_negbin,0.0369611144192673,0.0246797749499673,0.0529371411304404,0.147371614866085,0.0890058782232559,0.243896039032642,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,24.3943355167164,16.2886514669784,34.9385131460906,1.30837249415988,0.618537007570333,2.724644282244,0.394335516716403,0.308372494159881,No PCV +Netherlands.post.PCV7,23F,660,232251,4,2,0,adjusted_type_specific_negbin,0.00357297793889242,0.000813571450644751,0.00972831473251066,0.147371614866085,0.0890058782232559,0.243896039032642,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,2.358165439669,0.536957157425536,6.42068772345703,0.33683616061346,0.0715980322622597,1.05492838859573,0.358165439668998,0.33683616061346,PCV7 +Netherlands.post.PCV7,24B,660,232251,4,0,1,adjusted_type_specific_negbin,0.00133678474247497,0.000130100047131744,0.00564818502630014,0.147371614866085,0.0890058782232559,0.243896039032642,0.00341769534218185,0.000432780069399651,0.0397781644729013,3.54240797176599,2.49560124043154,5.15073328448319,0.882277930033479,0.0858660311069509,3.72780211735809,0.625103530909098,0.0560795461432311,4.17742114802704,0.882277930033479,0.374896469090902,No PCV +Netherlands.post.PCV7,24F,660,232251,4,3,1,adjusted_type_specific_negbin,0.00503131163265027,0.00164774942197202,0.0118497297842495,0.147371614866085,0.0890058782232559,0.243896039032642,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,3.32066567754918,1.08751461850153,7.82082165760467,1.50108066056865,0.441348516655837,4.40732696414677,0.320665677549176,0.501080660568651,No PCV +Netherlands.post.PCV7,27,660,232251,4,0,3,adjusted_type_specific_negbin,0.00252250661045403,0.000564947341843113,0.00757114140323083,0.147371614866085,0.0890058782232559,0.243896039032642,0.00450929445931807,0.00105355976436417,0.0191759279052972,3.54240797176599,2.49560124043154,5.15073328448319,1.66485436289966,0.372865245616455,4.99695332613235,1.51622798432945,0.34251927470978,5.72512475637734,1.66485436289966,1.48377201567055,No PCV +Netherlands.post.PCV7,3,660,232251,4,8,3,adjusted_type_specific_negbin,0.0127553289683779,0.00642014430606128,0.0225712329675852,0.147371614866085,0.0890058782232559,0.243896039032642,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,8.41851711912944,4.23729524200045,14.8970137586063,3.52486468351768,1.58366263823978,7.56394476026242,0.418517119129437,0.524864683517677,PCV13 +Netherlands.post.PCV7,31,660,232251,4,1,0,adjusted_type_specific_negbin,0.00230190719745494,0.000328868582763749,0.00768302748232413,0.147371614866085,0.0890058782232559,0.243896039032642,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,1.51925875032026,0.217053264624075,5.07079813833393,0.148169039692098,0.0175454959250389,0.721591001834815,0.519258750320258,0.148169039692098,No PCV +Netherlands.post.PCV7,33A,660,232251,4,2,0,adjusted_type_specific_negbin,0.00396448316443518,0.000871537210582413,0.0106467494062553,0.147371614866085,0.0890058782232559,0.243896039032642,1.83168515883687e-05,1.16579300526127e-06,0.000927087809352373,3.54240797176599,2.49560124043154,5.15073328448319,2.61655888852722,0.575214558984393,7.02685460812851,0.0095776493702387,0.000369259795009959,0.520723899332257,0.616558888527218,0.0095776493702387,No PCV +Netherlands.post.PCV7,33F,660,232251,4,7,1,adjusted_type_specific_negbin,0.0106731124683648,0.00500308192953168,0.0201910327462573,0.147371614866085,0.0890058782232559,0.243896039032642,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,7.0442542291208,3.30203407349091,13.3260816125298,1.94690705096518,0.744347083558632,4.74072820922557,0.0442542291207992,0.946907050965175,PCV15 +Netherlands.post.PCV7,35B,660,232251,4,9,0,adjusted_type_specific_negbin,0.0142392151662068,0.00708227721570964,0.0250027507769194,0.147371614866085,0.0890058782232559,0.243896039032642,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,9.39788200969652,4.67430296236836,16.5018155127668,0.251687911792816,0.0843213241960231,0.679168489194884,0.39788200969652,0.251687911792816,No PCV +Netherlands.post.PCV7,35F,660,232251,4,17,2,adjusted_type_specific_negbin,0.0284513808489569,0.017615652965293,0.043082410236006,0.147371614866085,0.0890058782232559,0.243896039032642,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,18.7779113603115,11.6263309570934,28.434390755764,0.582386632405024,0.223487463468055,1.3873259733445,1.77791136031153,1.41761336759498,No PCV +Netherlands.post.PCV7,36,660,232251,4,1,0,adjusted_type_specific_negbin,0.00246133238657799,0.000351199611599627,0.00820663326972939,0.147371614866085,0.0890058782232559,0.243896039032642,2.58839998099884e-05,1.1820498282222e-06,0.00170666709060845,3.54240797176599,2.49560124043154,5.15073328448319,1.62447937514148,0.231791743655754,5.4163779580214,0.00827202786009356,0.000205977068325103,0.582858805603861,0.624479375141475,0.00827202786009356,No PCV +Netherlands.post.PCV7,38,660,232251,4,3,0,adjusted_type_specific_negbin,0.00479581824178106,0.00139411082679325,0.0115919122264585,0.147371614866085,0.0890058782232559,0.243896039032642,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,3.1652400395755,0.920113145683545,7.65066206946258,0.571691717610467,0.136327012813729,1.87646922760625,0.1652400395755,0.571691717610467,No PCV +Netherlands.post.PCV7,4,660,232251,4,1,0,adjusted_type_specific_negbin,0.00189768357496758,0.000283123896166162,0.00646045695626469,0.147371614866085,0.0890058782232559,0.243896039032642,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,1.2524711594786,0.186861771469667,4.26390159113469,0.493036360422752,0.0692281273346334,1.92865570220159,0.252471159478604,0.493036360422752,PCV7 +Netherlands.post.PCV7,42,660,232251,4,1,0,adjusted_type_specific_negbin,0.00249486295272102,0.000348585688871303,0.00832192876200167,0.147371614866085,0.0890058782232559,0.243896039032642,1.64727034476203e-05,1.1485247591461e-06,0.000721087752303597,3.54240797176599,2.49560124043154,5.15073328448319,1.64660954879587,0.23006655465506,5.49247298292111,0.00535992602812741,0.000184406356931545,0.283909262068854,0.646609548795872,0.00535992602812741,No PCV +Netherlands.post.PCV7,6A,660,232251,4,25,0,adjusted_type_specific_negbin,0.0368826699491607,0.0244397303031798,0.0530040438818226,0.147371614866085,0.0890058782232559,0.243896039032642,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,24.3425621664461,16.1302220000987,34.9826689620029,2.18216109189981,1.12061482892048,4.21871664225466,0.657437833553907,2.18216109189981,PCV13 +Netherlands.post.PCV7,6B,660,232251,4,9,0,adjusted_type_specific_negbin,0.013140026702664,0.00645038258068482,0.0234733039223895,0.147371614866085,0.0890058782232559,0.243896039032642,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,8.67241762375825,4.25725250325198,15.4923805887771,1.34213759960774,0.573537764373096,2.92842567834594,0.327582376241747,1.34213759960774,PCV7 +Netherlands.post.PCV7,6C,660,232251,4,14,0,adjusted_type_specific_negbin,0.021817850243107,0.0125856134184815,0.0347416982566732,0.147371614866085,0.0890058782232559,0.243896039032642,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,14.3997811604506,8.30650485619781,22.9295208494043,0.24840913487103,0.0847444217935504,0.65879014645112,0.399781160450587,0.24840913487103,No PCV +Netherlands.post.PCV7,7F,660,232251,4,4,13,adjusted_type_specific_negbin,0.00816365012404366,0.00382930304496869,0.0157386571312444,0.147371614866085,0.0890058782232559,0.243896039032642,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,5.38800908186881,2.52734000967934,10.3875137066213,10.5322171241214,4.88323217039017,22.9332264549825,1.38800908186881,2.4677828758786,PCV10 +Netherlands.post.PCV7,8,660,232251,4,5,4,adjusted_type_specific_negbin,0.00985272440064409,0.00461089685376438,0.0184905762052414,0.147371614866085,0.0890058782232559,0.243896039032642,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,6.5027981044251,3.04319192348449,12.2037802954593,2.56801320800004,1.00541782042738,6.28415820061612,1.5027981044251,1.43198679199996,PCV20 +Netherlands.post.PCV7,9N,660,232251,4,2,0,adjusted_type_specific_negbin,0.00364080304270124,0.000826329450379613,0.00997590933391685,0.147371614866085,0.0890058782232559,0.243896039032642,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,2.40293000818282,0.545377437250544,6.58410016038512,0.257514507415658,0.0490337152414085,0.953829370859462,0.402930008182819,0.257514507415658,PPV23 +Netherlands.post.PCV7,9V,660,232251,4,1,1,adjusted_type_specific_negbin,0.00281488994387409,0.000624188466267809,0.00797642613573999,0.147371614866085,0.0890058782232559,0.243896039032642,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,1.8578273629569,0.411964387736754,5.26444124958839,0.781896168028521,0.164960678288877,2.56837808820139,0.8578273629569,0.218103831971479,PCV7 +Netherlands.pre.PCV,1,321,250924,2,1,4,adjusted_type_specific_negbin,0.00313068577322882,0.000827212169249471,0.0100243550319608,0.244530572603174,0.146640811096039,0.409923480595405,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,1.00495013320645,0.26553510632908,3.21781796525943,6.57752500318845,1.88296241081566,21.5339427449618,0.00495013320645121,2.57752500318845,PCV10 +Netherlands.pre.PCV,10A,321,250924,2,1,1,adjusted_type_specific_negbin,0.00637460577761671,0.00145378517242075,0.017612601014364,0.244530572603174,0.146640811096039,0.409923480595405,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,2.04624845461497,0.466665040347062,5.65364492561084,0.559938473102013,0.121325163501526,1.78175943178235,1.04624845461497,0.440061526897987,PCV20 +Netherlands.pre.PCV,11A,321,250924,2,10,0,adjusted_type_specific_negbin,0.0323016615207917,0.0166873906240466,0.0552478218128942,0.244530572603174,0.146640811096039,0.409923480595405,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,10.3688333481741,5.35665239031895,17.734550801939,0.264323378659015,0.0958768336609632,0.670060420236446,0.368833348174132,0.264323378659015,PCV20 +Netherlands.pre.PCV,14,321,250924,2,8,28,adjusted_type_specific_negbin,0.0330517693718602,0.0189032865665998,0.0534910593156723,0.244530572603174,0.146640811096039,0.409923480595405,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,10.6096179683671,6.06795498787853,17.1706300403308,17.0609740271242,9.29600374824608,31.4922700870123,2.60961796836712,10.9390259728758,PCV7 +Netherlands.pre.PCV,15A,321,250924,2,2,0,adjusted_type_specific_negbin,0.00722052750925613,0.00164862478033683,0.0198243157963888,0.244530572603174,0.146640811096039,0.409923480595405,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,2.31778933047122,0.529208554488122,6.3636053706408,0.365330078901996,0.076479233392078,1.22727020144074,0.317789330471217,0.365330078901996,No PCV +Netherlands.pre.PCV,15B/C,321,250924,2,10,2,adjusted_type_specific_negbin,0.034229189311853,0.0185567051421362,0.0565138433892914,0.244530572603174,0.146640811096039,0.409923480595405,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,10.9875697691048,5.95670235062571,18.1409437279626,1.46510418569102,0.663107229583663,3.0472016496315,0.987569769104802,0.534895814308983,PCV20 +Netherlands.pre.PCV,16F,321,250924,2,4,0,adjusted_type_specific_negbin,0.0127935533475286,0.00452455117899339,0.028472927753026,0.244530572603174,0.146640811096039,0.409923480595405,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,4.10673062455668,1.45238092845688,9.13980980872136,0.614141647539194,0.183383088806056,1.77172908937262,0.106730624556683,0.614141647539194,No PCV +Netherlands.pre.PCV,17F,321,250924,2,1,1,adjusted_type_specific_negbin,0.0070448601275747,0.00157576205301244,0.0194517759840615,0.244530572603174,0.146640811096039,0.409923480595405,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,2.26140010095148,0.505819619016994,6.24402009088375,0.328377048125532,0.0644864707920709,1.13318654089198,1.26140010095148,0.671622951874468,PPV23 +Netherlands.pre.PCV,18C,321,250924,2,4,6,adjusted_type_specific_negbin,0.015794532190571,0.00706287563856986,0.0310699937251283,0.244530572603174,0.146640811096039,0.409923480595405,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,5.07004483317329,2.26718307998092,9.97346798576618,5.1951028935144,2.21324146927476,12.1648200857003,1.07004483317329,0.804897106485599,PCV7 +Netherlands.pre.PCV,19A,321,250924,2,9,5,adjusted_type_specific_negbin,0.029522430619431,0.0156279636436677,0.0503446006132828,0.244530572603174,0.146640811096039,0.409923480595405,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,9.47670022883736,5.01657632961733,16.1606167968638,5.57899236810662,2.69191223651424,11.2426573904236,0.476700228837363,0.578992368106624,PCV13 +Netherlands.pre.PCV,19F,321,250924,2,24,4,adjusted_type_specific_negbin,0.0745166924382872,0.049991586586136,0.105043720493062,0.244530572603174,0.146640811096039,0.409923480595405,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,23.9198582726902,16.0472992941497,33.719034278273,5.87584170922045,3.11979034260628,11.0282471144019,0.0801417273098224,1.87584170922045,PCV7 +Netherlands.pre.PCV,21,321,250924,2,2,0,adjusted_type_specific_negbin,0.0076549417622813,0.00172887133410198,0.0209637363773903,0.244530572603174,0.146640811096039,0.409923480595405,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,2.4572363056923,0.554967698246735,6.7293593771423,0.184606831492198,0.0346282456097778,0.680668265472731,0.457236305692296,0.184606831492198,No PCV +Netherlands.pre.PCV,22F,321,250924,2,2,0,adjusted_type_specific_negbin,0.00630298679239986,0.00141788561175272,0.0174245876105772,0.244530572603174,0.146640811096039,0.409923480595405,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,2.02325876036036,0.455141281372622,5.59329262299528,0.790065288733129,0.165395432899597,2.52400066609398,0.0232587603603562,0.790065288733129,PCV15 +Netherlands.pre.PCV,23A,321,250924,2,1,1,adjusted_type_specific_negbin,0.00774324633754148,0.00179424717060763,0.0205565614498547,0.244530572603174,0.146640811096039,0.409923480595405,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,2.48558207435081,0.57595334176505,6.59865622540335,0.148075367263792,0.030723824943919,0.499495399965886,1.48558207435081,0.851924632736208,No PCV +Netherlands.pre.PCV,23B,321,250924,2,12,0,adjusted_type_specific_negbin,0.0366241726751774,0.0201627265767367,0.0606198712205933,0.244530572603174,0.146640811096039,0.409923480595405,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,11.7563594287319,6.47223523113247,19.4589786618105,1.16208061259777,0.488657127803055,2.63595484904878,0.243640571268056,1.16208061259777,No PCV +Netherlands.pre.PCV,23F,321,250924,2,28,4,adjusted_type_specific_negbin,0.0859158813992003,0.0597563965982654,0.117920286287964,0.244530572603174,0.146640811096039,0.409923480595405,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,27.5789979291433,19.1818033080432,37.8524118984365,7.25198121356573,3.92452322615378,13.5342783197894,0.421002070856694,3.25198121356573,PCV7 +Netherlands.pre.PCV,24F,321,250924,2,1,0,adjusted_type_specific_negbin,0.00316151271632962,0.000435758927513672,0.0114249934456445,0.244530572603174,0.146640811096039,0.409923480595405,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,1.01484558194181,0.139878615731889,3.66742289605188,0.846637113311422,0.114657391894376,3.4645793577175,0.0148455819418067,0.846637113311422,No PCV +Netherlands.pre.PCV,3,321,250924,2,3,1,adjusted_type_specific_negbin,0.00914156305465014,0.00294121381893159,0.0219408155054543,0.244530572603174,0.146640811096039,0.409923480595405,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,2.9344417405427,0.944129635877041,7.04300177725082,2.27859390735028,0.706057926770778,6.14580227288068,0.0655582594573039,1.27859390735028,PCV13 +Netherlands.pre.PCV,33F,321,250924,2,6,1,adjusted_type_specific_negbin,0.0176300465480915,0.00765852332463302,0.0349453771258115,0.244530572603174,0.146640811096039,0.409923480595405,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,5.65924494193739,2.4583859872072,11.2174660573855,2.87687956173679,1.06778229926215,7.14683145032491,0.340755058062614,1.87687956173679,PCV15 +Netherlands.pre.PCV,35B,321,250924,2,2,0,adjusted_type_specific_negbin,0.00782280217317542,0.00177562060552608,0.0214016174738246,0.244530572603174,0.146640811096039,0.409923480595405,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,2.51111949758931,0.569974214373872,6.86991920909768,0.123434618564558,0.0234877107803477,0.464185757139439,0.511119497589308,0.123434618564558,No PCV +Netherlands.pre.PCV,38,321,250924,2,1,0,adjusted_type_specific_negbin,0.00404078418931082,0.000578418926996749,0.0136541071267364,0.244530572603174,0.146640811096039,0.409923480595405,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,1.29709172476877,0.185672475565956,4.38296838768238,0.430881335923229,0.055583844392013,1.76477302457191,0.297091724768772,0.430881335923229,No PCV +Netherlands.pre.PCV,4,321,250924,2,1,2,adjusted_type_specific_negbin,0.00641180187771541,0.00170671249971312,0.0171820296498348,0.244530572603174,0.146640811096039,0.409923480595405,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,2.05818840274665,0.54785471240791,5.51543151759697,1.49497080582051,0.392327854542542,4.41041939084088,1.05818840274665,0.505029194179487,PCV7 +Netherlands.pre.PCV,6A,321,250924,2,25,5,adjusted_type_specific_negbin,0.0805739281973739,0.055249639807544,0.112929521976329,0.244530572603174,0.146640811096039,0.409923480595405,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,25.864230951357,17.7351343782216,36.2503765544017,4.28126096877825,2.3369785962815,7.88118871215425,0.864230951357015,0.718739031221751,PCV13 +Netherlands.pre.PCV,6B,321,250924,2,43,16,adjusted_type_specific_negbin,0.137589071216914,0.103603936302481,0.177264236645939,0.244530572603174,0.146640811096039,0.409923480595405,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,44.1660918606295,33.2568635530964,56.9018199633465,12.6353628837373,7.34127139576286,21.9960244346102,1.16609186062951,3.36463711626271,PCV7 +Netherlands.pre.PCV,7F,321,250924,2,0,8,adjusted_type_specific_negbin,0.00516418131968632,0.00176276999357766,0.013031221357735,0.244530572603174,0.146640811096039,0.409923480595405,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,1.65770220361931,0.565849167938428,4.18302205583293,5.98739233522966,2.21333054454617,15.4608202410727,1.65770220361931,2.01260766477034,PCV10 +Netherlands.pre.PCV,8,321,250924,2,0,2,adjusted_type_specific_negbin,0.00448574058813822,0.000940282511916109,0.0133926353115371,0.244530572603174,0.146640811096039,0.409923480595405,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,1.43992272879237,0.301830686325071,4.29903593500342,1.0525326881648,0.214265930386588,3.46323333563117,1.43992272879237,0.947467311835196,PCV20 +Netherlands.pre.PCV,9N,321,250924,2,1,1,adjusted_type_specific_negbin,0.00669935090283792,0.00156695285792006,0.0182349249262913,0.244530572603174,0.146640811096039,0.409923480595405,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,2.15049163981097,0.502991867392338,5.85341090133952,0.424726039593019,0.0849395255937713,1.5170629507859,1.15049163981097,0.575273960406981,PPV23 +Netherlands.pre.PCV,9V,321,250924,2,6,8,adjusted_type_specific_negbin,0.0235455946836644,0.0118300798375493,0.0416760069727261,0.244530572603174,0.146640811096039,0.409923480595405,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,7.55813589345627,3.79745562785332,13.3779982382451,5.87734061381835,2.70299621381049,12.6557982818819,1.55813589345627,2.12265938618165,PCV7 +Portugal.pre.PCV,1,1170,2071223,2,1,15,adjusted_type_specific_negbin,0.00341408527627403,0.00150700033800642,0.00692738774720093,0.0329508015765922,0.0201988890951475,0.05437118800636,0.017306487332837,0.00977434151305262,0.0313465265599201,3.54240797176599,2.49560124043154,5.15073328448319,3.99447977324062,1.76319039546751,8.10504366422509,8.02183016591586,3.7197407135948,16.9960873326061,2.99447977324062,6.97816983408414,PCV10 +Portugal.pre.PCV,10A,1170,2071223,2,19,2,adjusted_type_specific_negbin,0.0169446001518867,0.0108337290077714,0.0251385991181233,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,19.8251821777075,12.6754629390926,29.4121609682043,1.67208970051164,0.810612541218235,3.35229423580818,0.825182177707461,0.32791029948836,PCV20 +Portugal.pre.PCV,11A,1170,2071223,2,42,0,adjusted_type_specific_negbin,0.0361637845162782,0.0264277315429531,0.0477437504869824,0.0329508015765922,0.0201988890951475,0.05437118800636,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,42.3116278840455,30.9204459052551,55.8601880697694,0.333896480023277,0.142406378000525,0.735980724238099,0.311627884045514,0.333896480023277,PCV20 +Portugal.pre.PCV,14,1170,2071223,2,52,12,adjusted_type_specific_negbin,0.0436119121063582,0.03314539657377,0.0561809649011643,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,51.025937164439,38.7801139913109,65.7317289343623,25.2700451588953,14.6032713809262,44.7813157718568,0.974062835560957,13.2700451588953,PCV7 +Portugal.pre.PCV,15A,1170,2071223,2,4,0,adjusted_type_specific_negbin,0.00378782648275807,0.00132834819835613,0.00834851754338577,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,4.43175698482694,1.55416739207667,9.76776552576135,0.215183369360038,0.0631017449382477,0.610932435870572,0.43175698482694,0.215183369360038,No PCV +Portugal.pre.PCV,15B/C,1170,2071223,2,33,1,adjusted_type_specific_negbin,0.0285303758329281,0.0200500856893548,0.0391093275121377,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,33.3805397245259,23.4586002565452,45.7579131892012,1.36228413405193,0.717609545410013,2.55258553935015,0.380539724525867,0.36228413405193,PCV20 +Portugal.pre.PCV,16F,1170,2071223,2,36,0,adjusted_type_specific_negbin,0.0303950635370995,0.0217084913702938,0.0411306510515995,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,35.5622243384064,25.3989349032438,48.1228617303714,1.64048562949308,0.725402346583322,3.59181183377226,0.437775661593619,1.64048562949308,No PCV +Portugal.pre.PCV,18A,1170,2071223,2,12,0,adjusted_type_specific_negbin,0.0105516350576256,0.00568126319118145,0.0174426248981692,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000198001510080884,2.43125238691192e-05,0.000991711750205049,3.54240797176599,2.49560124043154,5.15073328448319,12.345413017422,6.64707793368229,20.407871130858,0.282054060216142,0.0337558800651674,1.46038293267897,0.345413017421958,0.282054060216142,No PCV +Portugal.pre.PCV,18C,1170,2071223,2,13,6,adjusted_type_specific_negbin,0.0122811407552848,0.00726171472532384,0.0193752757667088,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,14.3689346836832,8.49620622862889,22.6690726470493,4.54659431097376,2.21656878327391,9.44303105109154,1.36893468368318,1.45340568902624,PCV7 +Portugal.pre.PCV,19A,1170,2071223,2,45,11,adjusted_type_specific_negbin,0.0396535175597135,0.0296557495328065,0.0516151956321751,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,46.3946155448648,34.6972269533836,60.3897788896449,8.41027990182267,5.00452545883744,14.0963985588038,1.39461554486483,2.58972009817733,PCV13 +Portugal.pre.PCV,19F,1170,2071223,2,93,1,adjusted_type_specific_negbin,0.0783737614975028,0.0639309290523167,0.0946976619767256,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,91.6973009520783,74.7991869912105,110.796264512769,6.90226309383875,3.96089153055944,12.202493116411,1.30269904792172,5.90226309383875,PCV7 +Portugal.pre.PCV,20,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.00127165151081681,0.000179529486704573,0.00430843887953811,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,1.48783226765567,0.21004949944435,5.04087348905959,0.128258204231089,0.0136073434348647,0.691394268125297,1.48783226765567,0.871741795768911,PPV23 +Portugal.pre.PCV,21,1170,2071223,2,6,0,adjusted_type_specific_negbin,0.00555074435456515,0.00235003416623297,0.0108680600594414,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,6.49437089484122,2.74953997449258,12.7156302695465,0.150315790934003,0.0456697873477232,0.435743047133807,0.494370894841223,0.150315790934003,No PCV +Portugal.pre.PCV,22F,1170,2071223,2,8,0,adjusted_type_specific_negbin,0.00675456629234311,0.00320807097458913,0.012400150770704,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,7.90284256204144,3.75344304026928,14.5081764017236,0.945581017360864,0.371933899975607,2.2316017343921,0.0971574379585647,0.945581017360864,PCV15 +Portugal.pre.PCV,23A,1170,2071223,2,11,0,adjusted_type_specific_negbin,0.0097735251456637,0.00514763169092051,0.0165680900024556,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,11.4350244204265,6.022729078377,19.384665302873,0.211686017173045,0.0841381010104116,0.49750207239964,0.435024420426529,0.211686017173045,No PCV +Portugal.pre.PCV,23B,1170,2071223,2,11,1,adjusted_type_specific_negbin,0.0104463493163411,0.00569284249114898,0.0172298759346863,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,12.2222287001191,6.66062571464431,20.1589548435829,0.367468759194512,0.152902816881856,0.845987002153461,1.2222287001191,0.632531240805488,No PCV +Portugal.pre.PCV,23F,1170,2071223,2,70,13,adjusted_type_specific_negbin,0.0625316490838617,0.0498134689868722,0.0771610145799465,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,73.1620294281182,58.2817587146404,90.2783870585374,5.89714513709903,3.49278102397346,10.1384802699129,3.16202942811822,7.10285486290097,PCV7 +Portugal.pre.PCV,24F,1170,2071223,2,3,0,adjusted_type_specific_negbin,0.00259678240549075,0.000762695539006301,0.00630990206285862,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,3.03823541442418,0.892353780637372,7.38258541354458,0.77824189169413,0.196460587876827,2.40168442175448,0.0382354144241823,0.77824189169413,No PCV +Portugal.pre.PCV,3,1170,2071223,2,28,5,adjusted_type_specific_negbin,0.0240029811696952,0.0165125703964272,0.0335168315155652,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,28.0834879685434,19.3197073638198,39.2146928732113,6.67232976003085,3.5839812578368,12.516279295484,0.0834879685433876,1.67232976003085,PCV13 +Portugal.pre.PCV,31,1170,2071223,2,7,1,adjusted_type_specific_negbin,0.00692708740587326,0.00329161927161721,0.0126006454967178,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,8.10469226487171,3.85119454779213,14.7427552311599,0.456077116581179,0.129027879036414,1.41081456654727,1.10469226487171,0.543922883418821,No PCV +Portugal.pre.PCV,33F,1170,2071223,2,4,1,adjusted_type_specific_negbin,0.00414770024153634,0.00158838858312449,0.00865649220505713,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,4.85280928259751,1.85841464225565,10.1280958799168,0.754717065489226,0.247063713480179,1.96887898856065,0.852809282597514,0.245282934510774,PCV15 +Portugal.pre.PCV,34,1170,2071223,2,18,0,adjusted_type_specific_negbin,0.0157267662966349,0.00966577509187695,0.0239067765394026,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,18.4003165670628,11.308956857496,27.970928551101,0.213694395316529,0.0419381632402869,0.754609026808603,0.400316567062792,0.213694395316529,No PCV +Portugal.pre.PCV,35F,1170,2071223,2,35,1,adjusted_type_specific_negbin,0.0306924603198004,0.0219369678338826,0.0412721901684877,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,35.9101785741665,25.6662523656427,48.2884624971306,0.629756025814298,0.251125001827588,1.45885316123638,0.910178574166522,0.370243974185702,No PCV +Portugal.pre.PCV,37,1170,2071223,2,9,0,adjusted_type_specific_negbin,0.00813767938894467,0.0040658580606489,0.0143422735818197,0.0329508015765922,0.0201988890951475,0.05437118800636,8.73857936299313e-05,4.08275642783979e-06,0.000582177503837751,3.54240797176599,2.49560124043154,5.15073328448319,9.52108488506526,4.75705393095922,16.780460090729,0.0946016502945986,0.00426476642229323,0.677914919029926,0.521084885065259,0.0946016502945986,No PCV +Portugal.pre.PCV,4,1170,2071223,2,4,0,adjusted_type_specific_negbin,0.00337337355358714,0.00116972606842044,0.00753973807939858,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,3.94684705769695,1.36857950005192,8.82149355289634,0.882815201022808,0.269203603116596,2.39195818104133,0.0531529423030452,0.882815201022808,PCV7 +Portugal.pre.PCV,5,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.000760338424489105,0.000103552349943148,0.00288033565785984,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00734989518727071,0.00290832765960712,0.0190321029022971,3.54240797176599,2.49560124043154,5.15073328448319,0.889595956652253,0.121156249433483,3.36999271969601,0.751047715345387,0.0986187193049584,3.21266358907739,0.889595956652253,0.248952284654613,PCV10 +Portugal.pre.PCV,6A,1170,2071223,2,64,3,adjusted_type_specific_negbin,0.0551053393663238,0.043044649028349,0.0691178263757,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,64.4732470585989,50.3622393631683,80.867856859569,3.27513305827161,1.84961509322483,5.7670889454235,0.473247058598886,0.275133058271614,PCV13 +Portugal.pre.PCV,6B,1170,2071223,2,69,5,adjusted_type_specific_negbin,0.0591787591379301,0.0466260938404622,0.0736187823024383,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,69.2391481913782,54.5525297933408,86.1339752938528,6.07700726338984,3.52497551882355,10.6360313006931,0.239148191378192,1.07700726338984,PCV7 +Portugal.pre.PCV,6C,1170,2071223,2,14,0,adjusted_type_specific_negbin,0.0124206702271573,0.00714709282370383,0.0197931827891333,0.0329508015765922,0.0201988890951475,0.05437118800636,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,14.532184165774,8.36209860373348,23.158023863286,0.141008792593234,0.048765666278681,0.377735912034376,0.532184165774009,0.141008792593234,No PCV +Portugal.pre.PCV,7F,1170,2071223,2,3,4,adjusted_type_specific_negbin,0.00316831030283072,0.00124935217221654,0.00685680244551523,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,3.70692305431194,1.46174204149335,8.02245886125282,4.10205606180527,1.55234310443771,10.0316665662163,0.706923054311937,0.102056061805266,PCV10 +Portugal.pre.PCV,8,1170,2071223,2,1,1,adjusted_type_specific_negbin,0.00181920996149218,0.00041265000349019,0.00497991685873492,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,2.12847565494585,0.482800504083522,5.82650272471985,0.472373745074256,0.0981443787912234,1.61428864808959,1.12847565494585,0.527626254925744,PCV20 +Portugal.pre.PCV,9L,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.000959645682900997,0.000103475065890858,0.00370951220485282,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00268938450687417,0.000175749113163652,0.039503533475621,3.54240797176599,2.49560124043154,5.15073328448319,1.12278544899417,0.121065827092304,4.3401292796778,0.345784571422368,0.0180780915054229,2.97804340031048,1.12278544899417,0.654215428577632,No PCV +Portugal.pre.PCV,9N,1170,2071223,2,1,1,adjusted_type_specific_negbin,0.00209895533288965,0.000473903167721761,0.00581541254022699,0.0329508015765922,0.0201988890951475,0.05437118800636,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,2.4557777394809,0.554466706234461,6.80403267206558,0.148874855184678,0.027943916341934,0.56603231616247,1.4557777394809,0.851125144815322,PPV23 +Portugal.pre.PCV,9V,1170,2071223,2,14,2,adjusted_type_specific_negbin,0.0119181212990068,0.00691909718755241,0.0190203749657115,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,13.944201919838,8.09534370943632,22.2538387098824,3.33238904716223,1.51545145843489,7.29996116834447,0.055798080162015,1.33238904716223,PCV7 +Portugal.pre.PCV,19C,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.000602093972040467,2.34431624526773e-05,0.00311691944230773,0.0329508015765922,0.0201988890951475,0.05437118800636,0.00972772912616482,0.000210930671010865,0.411665900493469,3.54240797176599,2.49560124043154,5.15073328448319,0.704449947287346,0.0274285000696324,3.64679574750004,0.768127692803566,0.025826865489992,6.3673692368773,0.704449947287346,0.231872307196434,No PCV +E.W.pre.PCV,10A,3752,3091000,1,1,0,adjusted_type_specific_negbin,0.000294482348435988,4.26909444581158e-05,0.00103435138154133,1.07638532472038,0.679287032441144,1.72461984318033,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,1.10489777133183,0.16017642360685,3.88088638354307,0.705616783411854,0.100144308921614,2.69605990974401,0.104897771331828,0.705616783411854,PCV20 +E.W.pre.PCV,11A,3752,3091000,1,25,2,adjusted_type_specific_negbin,0.00691137469792207,0.00461011898394766,0.00988667323668673,1.07638532472038,0.679287032441144,1.72461984318033,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,25.9314778666036,17.2971664277716,37.0947979840486,1.56182237553798,0.67150533028092,3.34168704548392,0.931477866603593,0.438177624462019,PCV20 +E.W.pre.PCV,14,3752,3091000,1,58,125,adjusted_type_specific_negbin,0.0152725327108134,0.0117554831146112,0.0194765479034046,1.07638532472038,0.679287032441144,1.72461984318033,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,57.3025427309718,44.1065726460211,73.0760077335741,215.325715026004,128.875119286129,370.377571447007,0.69745726902817,90.3257150260036,PCV7 +E.W.pre.PCV,15B/C,3752,3091000,1,15,8,adjusted_type_specific_negbin,0.00449177956874081,0.00280596873928634,0.00682656081994046,1.07638532472038,0.679287032441144,1.72461984318033,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,16.8531569419155,10.5279947098024,25.6132561964166,5.20795135340223,2.77224438242448,9.80886172215484,1.85315694191551,2.79204864659777,PCV20 +E.W.pre.PCV,16F,3752,3091000,1,2,2,adjusted_type_specific_negbin,0.000884999077305244,0.000298951477617531,0.00201987081885931,1.07638532472038,0.679287032441144,1.72461984318033,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,3.32051653804927,1.12166594402098,7.57855531236013,1.15734880368076,0.347704217307019,3.17656771953071,1.32051653804927,0.842651196319244,No PCV +E.W.pre.PCV,17F,3752,3091000,1,0,1,adjusted_type_specific_negbin,0.000322254141736402,4.81701056494125e-05,0.00111019333272604,1.07638532472038,0.679287032441144,1.72461984318033,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,1.20909753979498,0.180734236396596,4.16544538438812,0.406695603611887,0.0580342549313827,1.61234439530472,1.20909753979498,0.593304396388113,PPV23 +E.W.pre.PCV,18B,3752,3091000,1,2,1,adjusted_type_specific_negbin,0.000524016413276814,0.000119732042756128,0.00149351084619364,1.07638532472038,0.679287032441144,1.72461984318033,0.00124945709832586,0.000238400207766176,0.00647740004764962,3.54240797176599,2.49560124043154,5.15073328448319,1.96610958261461,0.449234624420993,5.60365269491853,2.11445335802433,0.382280769191384,9.70737743782878,0.0338904173853947,1.11445335802433,No PCV +E.W.pre.PCV,18C,3752,3091000,1,12,41,adjusted_type_specific_negbin,0.00363529454544828,0.00216748791480397,0.0057732111576903,1.07638532472038,0.679287032441144,1.72461984318033,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,13.639625134522,8.13241465634448,21.661088263654,32.6895415766837,17.3385013822229,65.1747011491156,1.63962513452196,8.31045842331629,PCV7 +E.W.pre.PCV,19A,3752,3091000,1,18,20,adjusted_type_specific_negbin,0.00482176355089717,0.00302183399896362,0.00732823389741393,1.07638532472038,0.679287032441144,1.72461984318033,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,18.0912568429662,11.3379211641115,27.4955335830971,24.8334561011052,13.796771027399,44.8555880371001,0.0912568429661711,4.8334561011052,PCV13 +E.W.pre.PCV,19F,3752,3091000,1,92,52,adjusted_type_specific_negbin,0.0246961510379108,0.0201446069461745,0.0299939346999741,1.07638532472038,0.679287032441144,1.72461984318033,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,92.6599586942412,75.5825652620466,112.537242994303,52.9429229327007,32.3295067289487,90.3048657148236,0.659958694241183,0.942922932700725,PCV7 +E.W.pre.PCV,20,3752,3091000,1,0,1,adjusted_type_specific_negbin,0.0002577274880693,3.49340970020308e-05,0.000957800294647799,1.07638532472038,0.679287032441144,1.72461984318033,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,0.966993535236012,0.131072731951619,3.59366670551854,0.637633282319303,0.0788048170637519,2.94491887207402,0.966993535236012,0.362366717680697,PPV23 +E.W.pre.PCV,21,3752,3091000,1,4,0,adjusted_type_specific_negbin,0.00108469955080046,0.000371314269029614,0.00240817491408858,1.07638532472038,0.679287032441144,1.72461984318033,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,4.06979271460331,1.39317113739911,9.03547227766036,0.709916102833375,0.199774838321997,2.12594467864491,0.0697927146033104,0.709916102833375,No PCV +E.W.pre.PCV,22F,3752,3091000,1,11,9,adjusted_type_specific_negbin,0.00303927314589261,0.00170815778537479,0.00499638738745123,1.07638532472038,0.679287032441144,1.72461984318033,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,11.4033528433891,6.4090080107262,18.746445477717,10.3248083155214,5.02430083927054,21.2973473564173,0.403352843389072,1.32480831552143,PCV15 +E.W.pre.PCV,23A,3752,3091000,1,9,2,adjusted_type_specific_negbin,0.00269249934296002,0.00142038425703889,0.00458432052476484,1.07638532472038,0.679287032441144,1.72461984318033,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,10.102257534786,5.32928173240991,17.2003706089177,1.41820945070925,0.594674511736234,3.18858689495285,1.10225753478598,0.581790549290746,No PCV +E.W.pre.PCV,23F,3752,3091000,1,88,43,adjusted_type_specific_negbin,0.0234804726156298,0.0190017557767512,0.0285863463211477,1.07638532472038,0.679287032441144,1.72461984318033,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,88.0987332538428,71.2945876743704,107.255971396946,54.0691057326301,32.1869051721426,93.5507205749834,0.0987332538428376,11.0691057326301,PCV7 +E.W.pre.PCV,27,3752,3091000,1,1,1,adjusted_type_specific_negbin,0.000200395533796496,2.99365208885774e-05,0.000819232825985585,1.07638532472038,0.679287032441144,1.72461984318033,0.00450929445931807,0.00105355976436417,0.0191759279052972,3.54240797176599,2.49560124043154,5.15073328448319,0.751884042804455,0.112321826373942,3.07376156309791,2.85882759118798,0.511079230302011,13.9062721881653,0.248115957195545,1.85882759118798,No PCV +E.W.pre.PCV,3,3752,3091000,1,4,6,adjusted_type_specific_negbin,0.00114127626868126,0.000487451728431566,0.00235184800578353,1.07638532472038,0.679287032441144,1.72461984318033,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,4.28206856009208,1.82891888507524,8.82413371769981,7.70759156722921,3.20248724866596,17.8525829342528,0.282068560092078,1.70759156722921,PCV13 +E.W.pre.PCV,31,3752,3091000,1,1,0,adjusted_type_specific_negbin,0.000326099465763446,4.33028002851146e-05,0.0011414050525443,1.07638532472038,0.679287032441144,1.72461984318033,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,1.22352519554445,0.16247210666975,4.28255175714622,0.515973962257835,0.0608542655327904,2.31453019697292,0.223525195544449,0.515973962257835,No PCV +E.W.pre.PCV,35B,3752,3091000,1,4,1,adjusted_type_specific_negbin,0.00133395285065047,0.000508153350607294,0.00278264732068573,1.07638532472038,0.679287032441144,1.72461984318033,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,5.00499109564056,1.90659137147857,10.4404927472129,0.574620355026466,0.169329818321141,1.64216949159181,1.00499109564056,0.425379644973534,No PCV +E.W.pre.PCV,35F,3752,3091000,1,15,1,adjusted_type_specific_negbin,0.00400821693315177,0.00236134786456317,0.00632027045521948,1.07638532472038,0.679287032441144,1.72461984318033,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,15.0388299331854,8.85977718784101,23.7136547479835,1.98757174557887,0.783525524381312,4.76819612913799,0.0388299331854398,0.987571745578871,No PCV +E.W.pre.PCV,38,3752,3091000,1,1,3,adjusted_type_specific_negbin,0.000649619306646441,0.000195409715996688,0.00161643665364735,1.07638532472038,0.679287032441144,1.72461984318033,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,2.43737163853744,0.733177254419571,6.06487032448485,1.86896833723202,0.552299827555708,5.48001249258927,1.43737163853744,1.13103166276798,No PCV +E.W.pre.PCV,4,3752,3091000,1,0,10,adjusted_type_specific_negbin,0.00078141916889715,0.000316025551411922,0.00171613695470887,1.07638532472038,0.679287032441144,1.72461984318033,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,2.93188472170211,1.18572786889753,6.43894585406769,4.95513889001106,2.06970749062243,11.3429493497166,2.93188472170211,5.04486110998894,PCV7 +E.W.pre.PCV,6A,3752,3091000,1,82,16,adjusted_type_specific_negbin,0.0216452072438472,0.017279507554032,0.026604902460975,1.07638532472038,0.679287032441144,1.72461984318033,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,81.2128175789147,64.8327123427282,99.8215940335781,31.2594057413764,18.5072402429957,53.9117331380077,0.787182421085305,15.2594057413764,PCV13 +E.W.pre.PCV,6B,3752,3091000,1,186,64,adjusted_type_specific_negbin,0.0493602892045746,0.0427061355552992,0.0565899333727278,1.07638532472038,0.679287032441144,1.72461984318033,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,185.199805095564,160.233420603483,212.325430014475,123.134187160164,74.7975320795869,208.55753280707,0.800194904436239,59.1341871601638,PCV7 +E.W.pre.PCV,7F,3752,3091000,1,2,10,adjusted_type_specific_negbin,0.000500290617670406,0.000171783280832843,0.0013143554780119,1.07638532472038,0.679287032441144,1.72461984318033,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,1.87709039749936,0.644530869684828,4.93146175350064,15.703608409434,5.6462761384472,44.1261585217347,0.122909602500637,5.70360840943404,PCV10 +E.W.pre.PCV,8,3752,3091000,1,0,8,adjusted_type_specific_negbin,0.000673032341495152,0.000244509928982223,0.00155435328525894,1.07638532472038,0.679287032441144,1.72461984318033,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,2.52521734528981,0.917401253541302,5.83193352629155,4.24454061765174,1.63659888076593,10.6695406214247,2.52521734528981,3.75545938234826,PCV20 +E.W.pre.PCV,9N,3752,3091000,1,4,6,adjusted_type_specific_negbin,0.00169361298837367,0.000785122328687681,0.0032103749429501,1.07638532472038,0.679287032441144,1.72461984318033,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,6.35443593237801,2.94577897723618,12.0453267859488,2.95000851907475,1.14208249293309,7.235773877921,2.35443593237801,3.04999148092525,PPV23 +E.W.pre.PCV,9V,3752,3091000,1,11,28,adjusted_type_specific_negbin,0.00335041425600226,0.00194540220900336,0.00539659469809994,1.07638532472038,0.679287032441144,1.72461984318033,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,12.5707542885205,7.29914908818061,20.248023307271,22.8231201855996,11.8557203241188,45.3100978750042,1.57075428852047,5.17687981440043,PCV7 +France.post.PCV13,10A,1212,842076,2,11,14,adjusted_type_specific_negbin,0.00998474282903782,0.00572072076472832,0.0161338731441262,1.05661210231531,0.662693945538331,1.68949195587297,0.000724949122177665,0.000399899187832093,0.00130123990913038,3.54240797176599,2.49560124043154,5.15073328448319,12.1015083087938,6.93351356685072,19.554254250681,12.6965501747429,6.41779795010508,25.4856109999704,1.10150830879384,1.30344982525706,PCV20 +France.post.PCV13,10B,1212,842076,2,1,0,adjusted_type_specific_negbin,0.00084711529801814,0.000110330187418751,0.00324572921157921,1.05661210231531,0.662693945538331,1.68949195587297,0.000509389844494032,8.66360486448286e-05,0.00249463469166522,3.54240797176599,2.49560124043154,5.15073328448319,1.02670374119799,0.133720187151526,3.93382380443401,0.737646643124402,0.0725515090102977,4.19116756019811,0.0267037411979856,0.737646643124402,No PCV +France.post.PCV13,11A,1212,842076,2,13,2,adjusted_type_specific_negbin,0.0116331559768219,0.0067447519954573,0.0183759346369435,1.05661210231531,0.662693945538331,1.68949195587297,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,14.0993850439082,8.17463941849425,22.2716327799755,1.39021939244251,0.569063226164615,3.10500977634573,1.09938504390819,0.609780607557489,PCV20 +France.post.PCV13,11B,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000577380887485054,2.33224790041948e-05,0.00300331433938226,1.05661210231531,0.662693945538331,1.68949195587297,0.000798691335505034,1.71870602231671e-05,0.0341311775388045,3.54240797176599,2.49560124043154,5.15073328448319,0.699785635631885,0.0282668445530841,3.64001697933131,0.789379240509583,0.0258891127323999,6.58530722549104,0.699785635631885,0.210620759490417,No PCV +France.post.PCV13,11F,1212,842076,2,1,0,adjusted_type_specific_negbin,0.00125832302591617,0.000167417316316891,0.00432916811943609,1.05661210231531,0.662693945538331,1.68949195587297,1.75450713705624e-05,1.15584175091417e-06,0.00130519187429745,3.54240797176599,2.49560124043154,5.15073328448319,1.5250875074104,0.202909787376072,5.24695176075654,0.0389159894926614,0.00124775820631517,1.84689746580009,0.525087507410395,0.0389159894926614,No PCV +France.post.PCV13,12F,1212,842076,2,0,16,adjusted_type_specific_negbin,0.00126599787711582,0.000411661795777427,0.00335254687705183,1.05661210231531,0.662693945538331,1.68949195587297,0.00604185287379925,0.00279991943562254,0.0141061491643519,3.54240797176599,2.49560124043154,5.15073328448319,1.53438942706437,0.498934096482242,4.06328681498682,13.3299927764645,5.3874084100516,35.7489807212402,1.53438942706437,2.67000722353553,PCV20 +France.post.PCV13,14,1212,842076,2,2,2,adjusted_type_specific_negbin,0.000953556050130286,0.000242385690656832,0.00312287170499435,1.05661210231531,0.662693945538331,1.68949195587297,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,1.15570993275791,0.29377145707608,3.78492050645315,7.16237734543092,1.88545065455202,24.1011378413583,0.844290067242093,5.16237734543092,PCV7 +France.post.PCV13,15A,1212,842076,2,14,13,adjusted_type_specific_negbin,0.0129502593389872,0.00789688093168614,0.0199827951954213,1.05661210231531,0.662693945538331,1.68949195587297,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,15.6957143188524,9.5710196892036,24.2191477768506,9.53472283998195,4.78261192365674,19.2101433248084,1.69571431885243,3.46527716001805,No PCV +France.post.PCV13,15B/C,1212,842076,2,22,15,adjusted_type_specific_negbin,0.0192897110629517,0.0129527273689606,0.0275883981949731,1.05661210231531,0.662693945538331,1.68949195587297,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,23.3791298082974,15.6987055711803,33.4371386123074,11.9309436988608,6.60339462651348,21.8261831258247,1.37912980829742,3.06905630113924,PCV20 +France.post.PCV13,15F,1212,842076,2,0,2,adjusted_type_specific_negbin,0.00159105346011636,0.000336139035919279,0.00474515274791769,1.05661210231531,0.662693945538331,1.68949195587297,0.000170123300166289,2.02083655214776e-05,0.000864026455062348,3.54240797176599,2.49560124043154,5.15073328448319,1.92835679366102,0.407400511534166,5.75112513047623,0.463089464871894,0.0460344469322689,2.32807449851988,1.92835679366102,1.53691053512811,No PCV +France.post.PCV13,16F,1212,842076,2,3,1,adjusted_type_specific_negbin,0.00260502927297481,0.000848089998689201,0.00609062258884754,1.05661210231531,0.662693945538331,1.68949195587297,0.000396809553251291,0.000191384605800861,0.000802641191453472,3.54240797176599,2.49560124043154,5.15073328448319,3.15729547884547,1.02788507841131,7.38183457768321,1.81742092053431,0.535631635750344,5.03292147914365,0.157295478845474,0.817420920534314,No PCV +France.post.PCV13,17F,1212,842076,2,8,3,adjusted_type_specific_negbin,0.00664456547328928,0.00332059950964382,0.0119586402653806,1.05661210231531,0.662693945538331,1.68949195587297,0.000385326654007176,0.000177277845958622,0.000817525482393014,3.54240797176599,2.49560124043154,5.15073328448319,8.05321335362661,4.0245666056883,14.4938720016413,4.51212488369707,1.79146554247303,10.7851667187262,0.0532133536266137,1.51212488369707,PPV23 +France.post.PCV13,19A,1212,842076,2,8,16,adjusted_type_specific_negbin,0.0068635944383749,0.00359469346554402,0.0121403160311907,1.05661210231531,0.662693945538331,1.68949195587297,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,8.31867645931037,4.35676848023935,14.7140630298031,18.8380311858497,9.50160110728757,37.3198667871261,0.318676459310375,2.83803118584966,PCV13 +France.post.PCV13,19F,1212,842076,2,6,7,adjusted_type_specific_negbin,0.00572056396586266,0.00281934251723522,0.0104198948803774,1.05661210231531,0.662693945538331,1.68949195587297,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,6.93332352662554,3.41704313088908,12.6289125950174,6.51954049769944,2.9688818496663,13.6611757682409,0.933323526625545,0.480459502300558,PCV7 +France.post.PCV13,2,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000241483275442877,1.25432592185652e-05,0.00185381940788207,1.05661210231531,0.662693945538331,1.68949195587297,0.00396667808056597,0.000257626265044538,0.0519109501755693,3.54240797176599,2.49560124043154,5.15073328448319,0.292677729836767,0.015202430172901,2.24682912235306,1.56608837155803,0.156566529374085,9.87987078749316,0.292677729836767,0.566088371558034,PPV23 +France.post.PCV13,20,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000753794117534841,9.83610846662374e-05,0.00299177782672453,1.05661210231531,0.662693945538331,1.68949195587297,0.000764947814335124,0.000205921000405982,0.00259402357512921,3.54240797176599,2.49560124043154,5.15073328448319,0.913598470452228,0.11921363461548,3.62603472599013,0.989293934092645,0.12589997827881,4.75420785471578,0.0864015295477722,0.989293934092645,PPV23 +France.post.PCV13,21,1212,842076,2,3,3,adjusted_type_specific_negbin,0.00395368929678352,0.00158094648450426,0.00818150445945386,1.05661210231531,0.662693945538331,1.68949195587297,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,4.79187142770162,1.91610713921917,9.91598340485808,1.38254394716696,0.470192880283464,3.66961929427853,1.79187142770162,1.61745605283304,No PCV +France.post.PCV13,22F,1212,842076,2,6,9,adjusted_type_specific_negbin,0.00544004347777912,0.0026417154466703,0.00993738725635533,1.05661210231531,0.662693945538331,1.68949195587297,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,6.59333269506829,3.2017591213644,12.0441133547027,9.84510072160381,4.47729567946541,21.3500623654359,0.593332695068289,0.845100721603814,PCV15 +France.post.PCV13,23A,1212,842076,2,9,4,adjusted_type_specific_negbin,0.0087249470420987,0.00474281474007548,0.0146379544604058,1.05661210231531,0.662693945538331,1.68949195587297,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,10.5746358150236,5.74829146497148,17.7412008060119,2.44810545125601,1.07267967562876,5.31499994846209,1.57463581502362,1.55189454874399,No PCV +France.post.PCV13,23B,1212,842076,2,15,2,adjusted_type_specific_negbin,0.01184387854693,0.0069448778230042,0.0187839573513985,1.05661210231531,0.662693945538331,1.68949195587297,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,14.3547807988791,8.41719192148109,22.766156309895,5.42182319163533,2.5120349239313,11.656059418758,0.645219201120895,3.42182319163533,No PCV +France.post.PCV13,24A,1212,842076,2,1,1,adjusted_type_specific_negbin,0.00137878163987666,0.000197386675568146,0.0046155646868012,1.05661210231531,0.662693945538331,1.68949195587297,0.000324684008602983,8.95359673303925e-06,0.00572558971878747,3.54240797176599,2.49560124043154,5.15073328448319,1.67108334753052,0.239232650788593,5.59406440040305,0.770329364002857,0.0280100846177228,6.59754438845418,0.671083347530517,0.229670635997143,No PCV +France.post.PCV13,24F,1212,842076,2,6,36,adjusted_type_specific_negbin,0.00668729216156913,0.00347270547730524,0.0117640822482169,1.05661210231531,0.662693945538331,1.68949195587297,0.00221225480824379,0.0010413936539902,0.00480515098840437,3.54240797176599,2.49560124043154,5.15073328448319,8.10499809982178,4.20891903849395,14.2580676848389,25.771916000611,12.641947704926,55.8917133278497,2.10499809982178,10.228083999389,No PCV +France.post.PCV13,25A,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000543663021809223,6.49110771317782e-05,0.00231868611010212,1.05661210231531,0.662693945538331,1.68949195587297,0.00165141051651395,0.000589976401575755,0.00500660807717493,3.54240797176599,2.49560124043154,5.15073328448319,0.658919582432778,0.0786722254837152,2.81024756544377,1.56855448799033,0.19351598147544,7.54158243532634,0.341080417567222,1.56855448799033,No PCV +France.post.PCV13,29,1212,842076,2,1,1,adjusted_type_specific_negbin,0.00190147369957937,0.000417065017463726,0.00533385349194158,1.05661210231531,0.662693945538331,1.68949195587297,6.39161619681567e-05,3.15448575829138e-06,0.000496397918354293,3.54240797176599,2.49560124043154,5.15073328448319,2.3045861238902,0.505482801166036,6.46463043223319,0.202236385182563,0.00943008005398166,1.59573101268585,1.3045861238902,0.797763614817437,No PCV +France.post.PCV13,3,1212,842076,2,1,5,adjusted_type_specific_negbin,0.00145504129466213,0.000475416003544682,0.00373049847484134,1.05661210231531,0.662693945538331,1.68949195587297,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,1.76351004913051,0.576204196296154,4.52136415150771,5.25194107128941,1.79286803980988,14.3337619806933,0.763510049130505,0.251941071289414,PCV13 +France.post.PCV13,31,1212,842076,2,2,1,adjusted_type_specific_negbin,0.00188428289451863,0.000512492396723772,0.00500888264756501,1.05661210231531,0.662693945538331,1.68949195587297,0.000487508830110507,0.000169293255028087,0.00127246203929191,3.54240797176599,2.49560124043154,5.15073328448319,2.28375086815658,0.621140784829212,6.07076576884879,1.58891179728603,0.374458897141581,5.45806946095306,0.283750868156584,0.588911797286034,No PCV +France.post.PCV13,33F,1212,842076,2,3,6,adjusted_type_specific_negbin,0.00290008244415447,0.00115768711963399,0.00626771756151287,1.05661210231531,0.662693945538331,1.68949195587297,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,3.51489992231522,1.4031167889964,7.5964736845536,6.82246400657395,2.66382237657069,16.8770260748332,0.51489992231522,0.822464006573954,PCV15 +France.post.PCV13,34,1212,842076,2,1,0,adjusted_type_specific_negbin,0.00120428553739187,0.000175026026818378,0.0040547140617008,1.05661210231531,0.662693945538331,1.68949195587297,0.000100522243695588,2.11909492164257e-05,0.000326088950875353,3.54240797176599,2.49560124043154,5.15073328448319,1.45959407131895,0.212131544503874,4.91431344278137,0.203765569747747,0.0208378633634714,1.09722693931442,0.459594071318946,0.203765569747747,No PCV +France.post.PCV13,35B,1212,842076,2,7,4,adjusted_type_specific_negbin,0.00751754560564712,0.00382631524522848,0.0132865221222724,1.05661210231531,0.662693945538331,1.68949195587297,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,9.11126527404431,4.63749407721692,16.1032648121942,1.73283860391287,0.655770118465455,4.19498000899102,2.11126527404431,2.26716139608713,No PCV +France.post.PCV13,35F,1212,842076,2,4,2,adjusted_type_specific_negbin,0.0043710955908163,0.00178816962643563,0.00878191680173306,1.05661210231531,0.662693945538331,1.68949195587297,0.000150455744934267,6.39397500030814e-05,0.000328279283660717,3.54240797176599,2.49560124043154,5.15073328448319,5.29776785606935,2.16726158723998,10.6436831637005,1.14591314100435,0.376882991393824,3.06307941483423,1.29776785606935,0.854086858995647,No PCV +France.post.PCV13,38,1212,842076,2,0,5,adjusted_type_specific_negbin,0.00171425134239744,0.000536537934117627,0.00432122596337932,1.05661210231531,0.662693945538331,1.68949195587297,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,2.0776726269857,0.650283976150564,5.23732586761573,2.63418065747045,0.840741014568934,7.29314090971362,2.0776726269857,2.36581934252955,No PCV +France.post.PCV13,4,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000411593377968701,5.09208207974268e-05,0.0018034236865837,1.05661210231531,0.662693945538331,1.68949195587297,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,0.498851174098065,0.0617160348064812,2.18574950813945,1.39542273555483,0.177107201843677,6.10620313937236,0.498851174098065,0.395422735554827,PCV7 +France.post.PCV13,6A,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000827931339797436,0.000111550900717876,0.00294694208071933,1.05661210231531,0.662693945538331,1.68949195587297,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,1.00345278383449,0.135199691670065,3.57169380183183,0.636783016169143,0.0873124841112563,2.42989646920067,1.00345278383449,0.363216983830857,PCV13 +France.post.PCV13,6B,1212,842076,2,2,0,adjusted_type_specific_negbin,0.00129393968524309,0.000267164442112713,0.00390091660836518,1.05661210231531,0.662693945538331,1.68949195587297,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,1.56825489851463,0.323803303840608,4.7279109293386,1.72426416787374,0.351395986839932,5.67307743301499,0.431745101485369,1.72426416787374,PCV7 +France.post.PCV13,6C,1212,842076,2,6,1,adjusted_type_specific_negbin,0.00558461145682261,0.00245677656376947,0.0106903298109248,1.05661210231531,0.662693945538331,1.68949195587297,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,6.768549085669,2.9776131952886,12.9566797308409,0.819390051412103,0.259004362393639,2.29169204856179,0.768549085669003,0.180609948587897,No PCV +France.post.PCV13,7C,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000846631789831215,0.000116438834251323,0.00310933436707726,1.05661210231531,0.662693945538331,1.68949195587297,0.000395968078807268,0.000112206548547661,0.00124464123083086,3.54240797176599,2.49560124043154,5.15073328448319,1.02611772927543,0.141123867112604,3.76851325289764,0.572837600003419,0.0714960048673964,2.70499957440829,1.02611772927543,0.427162399996581,No PCV +France.post.PCV13,7F,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000187017206875515,1.90840650579921e-05,0.00115601879544148,1.05661210231531,0.662693945538331,1.68949195587297,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,0.226664854733125,0.0231298868502864,1.40109478007507,3.15429898934032,0.341848724992462,20.0372802515991,0.773335145266875,3.15429898934032,PCV10 +France.post.PCV13,9N,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000863591674958002,0.000122140424023645,0.00312935268302547,1.05661210231531,0.662693945538331,1.68949195587297,0.000529002688683255,0.000217874616037613,0.00123839358388801,3.54240797176599,2.49560124043154,5.15073328448319,1.0466731100491,0.148034193916657,3.79277545182687,0.795790021918719,0.10549075484159,3.42127728918102,0.046673110049098,0.795790021918719,PPV23 +Atlanta.post.PCV7,11A,451,298831,1,10,0,adjusted_type_specific_negbin,0.0227635798271377,0.0118792374993298,0.039029389825449,0.874100846750956,0.456606835827787,1.68336087032668,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,10.2663745020391,5.35753611219774,17.6022548112775,0.39712969055911,0.135004592389153,1.07639367683721,0.266374502039081,0.39712969055911,PCV20 +Atlanta.post.PCV7,12F,451,298831,1,0,1,adjusted_type_specific_negbin,0.000944037374906532,0.000108242578989983,0.00444637802038201,0.874100846750956,0.456606835827787,1.68336087032668,0.00604185287379925,0.00279991943562254,0.0141061491643519,3.54240797176599,2.49560124043154,5.15073328448319,0.425760856082846,0.0488174031244822,2.00531648719229,1.48267818198929,0.18755265972786,6.99830629271664,0.425760856082846,0.482678181989294,PCV20 +Atlanta.post.PCV7,13,451,298831,1,0,1,adjusted_type_specific_negbin,0.00254019115214305,0.000350261005354125,0.00912676097630529,0.874100846750956,0.456606835827787,1.68336087032668,0.000641136431718939,0.000181165818687303,0.00210187050439682,3.54240797176599,2.49560124043154,5.15073328448319,1.14562620961651,0.15796771341471,4.11616920031369,0.414466338955325,0.0485654002559429,2.06437543216291,1.14562620961651,0.585533661044675,No PCV +Atlanta.post.PCV7,15A,451,298831,1,4,0,adjusted_type_specific_negbin,0.0086287347729171,0.0030164709504235,0.019238324961581,0.874100846750956,0.456606835827787,1.68336087032668,0.000417527980179903,0.000218575301339506,0.000798783879697387,3.54240797176599,2.49560124043154,5.15073328448319,3.89155938258561,1.360428398641,8.67648455767301,0.930968927909976,0.265469587502672,2.75456951506298,0.108440617414388,0.930968927909976,No PCV +Atlanta.post.PCV7,15B/C,451,298831,1,8,3,adjusted_type_specific_negbin,0.0207140077899927,0.0105772216604172,0.0360369131231326,0.874100846750956,0.456606835827787,1.68336087032668,0.000350450029963272,0.000206561593111568,0.000592659860950978,3.54240797176599,2.49560124043154,5.15073328448319,9.34201751328669,4.77032696884817,16.2526478185328,1.88186573678459,0.785449166509245,4.26034280018539,1.34201751328669,1.11813426321541,PCV20 +Atlanta.post.PCV7,19A,451,298831,1,29,23,adjusted_type_specific_negbin,0.0650020801219387,0.0458503603098646,0.089354440948345,0.874100846750956,0.456606835827787,1.68336087032668,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,29.3159381349943,20.6785124997489,40.2988528677036,26.1077303453027,13.6435896401116,51.6999884522319,0.315938134994347,3.10773034530266,PCV13 +Atlanta.post.PCV7,19F,451,298831,1,1,0,adjusted_type_specific_negbin,0.00279896312051369,0.000385148615287765,0.00976604119935076,0.874100846750956,0.456606835827787,1.68336087032668,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,1.26233236735167,0.173702025494782,4.40448458090719,0.467966349927,0.0615728275315487,1.8543534804893,0.262332367351675,0.467966349927,PCV7 +Atlanta.post.PCV7,21,451,298831,1,3,2,adjusted_type_specific_negbin,0.0107679035583835,0.00413952991104232,0.0225741850250004,0.874100846750956,0.456606835827787,1.68336087032668,0.000201191723053622,8.63910480193485e-05,0.00043740678905833,3.54240797176599,2.49560124043154,5.15073328448319,4.85632450483097,1.86692798988009,10.1809574462752,0.556405979796329,0.155828588960688,1.66838846338058,1.85632450483097,1.44359402020367,No PCV +Atlanta.post.PCV7,22F,451,298831,1,0,2,adjusted_type_specific_negbin,0.00342276149782883,0.000755341864868445,0.00992354689912779,0.874100846750956,0.456606835827787,1.68336087032668,0.00102956781356302,0.000579433867526241,0.001867676643371,3.54240797176599,2.49560124043154,5.15073328448319,1.5436654355208,0.340659181055669,4.47551965150663,0.915411070135228,0.194125377319997,2.97509366993197,1.5436654355208,1.08458892986477,PCV15 +Atlanta.post.PCV7,23A,451,298831,1,10,0,adjusted_type_specific_negbin,0.0220637491050054,0.0113085484932418,0.037742423756185,0.874100846750956,0.456606835827787,1.68336087032668,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,9.95075084635743,5.10015537045207,17.0218331140394,0.90629760766022,0.331104180888921,2.34209379167745,0.0492491536425703,0.90629760766022,No PCV +Atlanta.post.PCV7,23B,451,298831,1,10,1,adjusted_type_specific_negbin,0.0227402272657669,0.0120125568683306,0.0386570971035992,0.874100846750956,0.456606835827787,1.68336087032668,0.000260242673593068,0.000136973541701533,0.000481293243806414,3.54240797176599,2.49560124043154,5.15073328448319,10.2558424968609,5.4176631476171,17.4343507937232,1.52856392852452,0.595788551258668,3.71553240748632,0.255842496860861,0.528563928524523,No PCV +Atlanta.post.PCV7,3,451,298831,1,0,1,adjusted_type_specific_negbin,0.00173579090945509,0.000215482901115399,0.0066448312854218,0.874100846750956,0.456606835827787,1.68336087032668,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,0.782841700164247,0.097182788403045,2.99681890972523,0.91587358408706,0.114887285123435,3.7423856184128,0.782841700164247,0.0841264159129405,PCV13 +Atlanta.post.PCV7,33F,451,298831,1,5,6,adjusted_type_specific_negbin,0.013814672612655,0.00642494315558328,0.0261018866989554,0.874100846750956,0.456606835827787,1.68336087032668,0.00134331055960442,0.000701536413990498,0.00260362714263321,3.54240797176599,2.49560124043154,5.15073328448319,6.23041734830739,2.89764936316806,11.7719509012289,4.77432943424146,1.96781182708276,11.5089283237818,1.23041734830739,1.22567056575854,PCV15 +Atlanta.post.PCV7,35B,451,298831,1,14,1,adjusted_type_specific_negbin,0.0322085624874394,0.0187763874344986,0.0504168468784764,0.874100846750956,0.456606835827787,1.68336087032668,0.000130789512742347,5.64560410836904e-05,0.000282207167203243,3.54240797176599,2.49560124043154,5.15073328448319,14.5260616818352,8.46815073295889,22.7379979421929,1.08665598718363,0.388622249236604,2.84705657659462,0.526061681835188,0.086655987183631,No PCV +Atlanta.post.PCV7,38,451,298831,1,0,2,adjusted_type_specific_negbin,0.00353784938933892,0.000781981409312454,0.0105792363635582,0.874100846750956,0.456606835827787,1.68336087032668,0.000884785485051211,0.000378174145678876,0.00198873940303258,3.54240797176599,2.49560124043154,5.15073328448319,1.59557007459185,0.352673615599917,4.77123559996476,0.806464066163562,0.161318873440256,2.86370757547018,1.59557007459185,1.19353593383644,No PCV +Atlanta.post.PCV7,6C,451,298831,1,23,0,adjusted_type_specific_negbin,0.0504671707242236,0.033049844654825,0.0730684374731382,0.874100846750956,0.456606835827787,1.68336087032668,8.36527546995498e-05,3.31864675469349e-05,0.000199018240299565,3.54240797176599,2.49560124043154,5.15073328448319,22.7606939966249,14.9054799393261,32.9538653003853,1.09886813262281,0.380300236328,2.9596640007847,0.239306003375148,1.09886813262281,No PCV +Atlanta.post.PCV7,7F,451,298831,1,0,4,adjusted_type_specific_negbin,0.00171349460240001,0.000406825998066817,0.0057902527734174,0.874100846750956,0.456606835827787,1.68336087032668,0.00955577920275352,0.00558926749776212,0.016678469993424,3.54240797176599,2.49560124043154,5.15073328448319,0.772786065682406,0.183478525128134,2.61140400081125,4.2393212667562,1.11790308015173,14.2907714161287,0.772786065682406,0.239321266756201,PCV10 +Atlanta.pre.PCV,11A,231,204680,1,5,0,adjusted_type_specific_negbin,0.0218046839465464,0.00844181081779802,0.0450026008176762,2.42643155887219,1.36556313068154,4.49093474170449,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,5.03688199165221,1.95005829891134,10.3956007888832,0.722339537443708,0.220192037986043,2.04228550128496,0.0368819916522067,0.722339537443708,PCV20 +Atlanta.pre.PCV,14,231,204680,1,3,67,adjusted_type_specific_negbin,0.0226471540405124,0.0111123126120801,0.0427235527983883,2.42643155887219,1.36556313068154,4.49093474170449,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,5.23149258335836,2.56694421339049,9.86914069642769,47.4148443292297,24.3511486016554,96.7916508205608,2.23149258335836,19.5851556707703,PCV7 +Atlanta.pre.PCV,18C,231,204680,1,0,4,adjusted_type_specific_negbin,0.00319225843310319,0.000782577457100247,0.0107933498567324,2.42643155887219,1.36556313068154,4.49093474170449,0.00273207102148264,0.00146697046533674,0.00520504850783388,3.54240797176599,2.49560124043154,5.15073328448319,0.737411698046838,0.180775392590157,2.49326381690517,4.33590886387906,1.18211461364532,14.7470170038142,0.737411698046838,0.335908863879057,PCV7 +Atlanta.pre.PCV,19A,231,204680,1,8,9,adjusted_type_specific_negbin,0.0299048432973493,0.0143458431466859,0.0558095436483,2.42643155887219,1.36556313068154,4.49093474170449,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,6.90801880168768,3.31388976688445,12.8920045827573,22.8551752887079,9.99944105019157,52.3964551860113,1.09198119831232,13.8551752887079,PCV13 +Atlanta.pre.PCV,19F,231,204680,1,11,30,adjusted_type_specific_negbin,0.0583033193362964,0.0352388271860575,0.0904729728475744,2.42643155887219,1.36556313068154,4.49093474170449,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,13.4680667666845,8.14016907997929,20.8992567277897,18.5784233862629,10.0915811117924,35.3517520384065,2.46806676668448,11.4215766137371,PCV7 +Atlanta.pre.PCV,23F,231,204680,1,17,23,adjusted_type_specific_negbin,0.0751521273958067,0.0476814356620173,0.111663952306114,2.42643155887219,1.36556313068154,4.49093474170449,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,17.3601414284313,11.014411637926,25.7943729827124,25.7500676057814,13.4591031472896,51.194013831619,0.360141428431341,2.7500676057814,PCV7 +Atlanta.pre.PCV,4,231,204680,1,0,10,adjusted_type_specific_negbin,0.00768091935672823,0.00263358338872921,0.0192158099892257,2.42643155887219,1.36556313068154,4.49093474170449,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,1.77429237140422,0.608357762796447,4.43885210751113,7.19215477196183,2.80512100763258,18.6748529354417,1.77429237140422,2.80784522803817,PCV7 +Atlanta.pre.PCV,6A,231,204680,1,15,15,adjusted_type_specific_negbin,0.0681803535678555,0.0419366160489588,0.103133908548285,2.42643155887219,1.36556313068154,4.49093474170449,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,15.7496616741746,9.68735830730949,23.8239328746538,14.5950864887207,7.64532822794652,28.7700701918791,0.749661674174618,0.404913511279322,PCV13 +Atlanta.pre.PCV,6B,231,204680,1,17,24,adjusted_type_specific_negbin,0.0748170155847395,0.047648744545285,0.111281091974139,2.42643155887219,1.36556313068154,4.49093474170449,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,17.2827306000748,11.0068599899608,25.7059322460262,27.6966699615242,14.6798405173488,55.2582574671226,0.282730600074821,3.69666996152419,PCV7 +Atlanta.pre.PCV,9V,231,204680,1,6,10,adjusted_type_specific_negbin,0.0221821632203724,0.00972246073600949,0.0445044021855204,2.42643155887219,1.36556313068154,4.49093474170449,0.00206598279845095,0.00108251944299008,0.00392155680810816,3.54240797176599,2.49560124043154,5.15073328448319,5.12407970390603,2.24588843001819,10.2805169048552,22.4416837883368,9.05058547928524,56.7157882166432,0.87592029609397,12.4416837883368,PCV7 +Ontario.pre.PCV,11A,1139,580507,1,26,0,adjusted_type_specific_negbin,0.0231625885227621,0.015590497256555,0.03279757441584,0.308132555128898,0.163661481760943,0.593496824401793,6.77785666409278e-05,3.10752567574189e-05,0.000137947752239885,3.54240797176599,2.49560124043154,5.15073328448319,26.3821883274261,17.7575763752162,37.3564372596417,0.278216163869526,0.106050509255606,0.680296634454863,0.382188327426057,0.278216163869526,PCV20 +Ontario.pre.PCV,14,1139,580507,1,30,36,adjusted_type_specific_negbin,0.0287541450724716,0.0204397676606381,0.039045851748778,0.308132555128898,0.163661481760943,0.593496824401793,0.00425720451814257,0.00258389265675727,0.00699992895958463,3.54240797176599,2.49560124043154,5.15073328448319,32.7509712375452,23.2808953654667,44.4732251418582,21.6761294483017,11.9903270034253,40.5413890398028,2.75097123754519,14.3238705516983,PCV7 +Ontario.pre.PCV,19A,1139,580507,1,16,2,adjusted_type_specific_negbin,0.0138532749645489,0.00830179820498486,0.0214593466932738,0.308132555128898,0.163661481760943,0.593496824401793,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,15.7788801846211,9.45574815547776,24.4421958836389,3.81924965072961,1.8061397867839,7.983474342632,0.221119815378852,1.81924965072961,PCV13 +Ontario.pre.PCV,19F,1139,580507,1,71,9,adjusted_type_specific_negbin,0.0633356796709288,0.0502980993289737,0.0783028079016891,0.308132555128898,0.163661481760943,0.593496824401793,0.00064628051752876,0.000388588816569185,0.00106958621440333,3.54240797176599,2.49560124043154,5.15073328448319,72.1393391451879,57.2895351357011,89.1868982000238,7.28308114837808,3.89786900891983,14.1665997760593,1.13933914518789,1.71691885162192,PCV7 +Ontario.pre.PCV,23F,1139,580507,1,94,9,adjusted_type_specific_negbin,0.0827660460666321,0.0676861696822765,0.099879503116193,0.308132555128898,0.163661481760943,0.593496824401793,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,94.2705264698939,77.0945472681129,113.762754049344,10.2070676645504,5.37946278093823,20.0136118874956,0.270526469893909,1.20706766455035,PCV7 +Ontario.pre.PCV,6A,1139,580507,1,67,2,adjusted_type_specific_negbin,0.0584117742550935,0.045924311461439,0.0726571368181421,0.308132555128898,0.163661481760943,0.593496824401793,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,66.5310108765515,52.307790754579,82.7564788358639,4.52293445276939,2.29434470569194,8.99909927530062,0.468989123448495,2.52293445276939,PCV13 +Ontario.pre.PCV,6B,1139,580507,1,108,11,adjusted_type_specific_negbin,0.0949619997819492,0.0791217708245436,0.112850153623489,0.308132555128898,0.163661481760943,0.593496824401793,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,108.16171775164,90.1196969691552,128.536324977154,12.7267525802082,6.83696020863618,24.3193388514113,0.161717751640083,1.72675258020824,PCV7 +Morocco.pre.PCV,19A,200,212566,1,0,10,adjusted_type_specific_negbin,0.0076132129008636,0.00256399832644528,0.0199941027895684,3.20951415463519,1.60527496510844,6.71737424952721,0.00155276860126482,0.00100526519787505,0.00241499994716684,3.54240797176599,2.49560124043154,5.15073328448319,1.52264258017272,0.512799665289056,3.99882055791368,8.02226774877565,3.04997826802429,21.1690512960143,1.52264258017272,1.97773225122435,PCV13 +Morocco.pre.PCV,23A,200,212566,1,5,6,adjusted_type_specific_negbin,0.0338595084828308,0.0163199494208638,0.0618675007122317,3.20951415463519,1.60527496510844,6.71737424952721,0.000159489643548523,7.97250367814063e-05,0.000309150509489076,3.54240797176599,2.49560124043154,5.15073328448319,6.77190169656615,3.26398988417276,12.3735001424463,3.64320353830716,1.48957653975571,8.73559418504963,1.77190169656615,2.35679646169284,No PCV +Morocco.pre.PCV,23F,200,212566,1,3,11,adjusted_type_specific_negbin,0.0207309100758813,0.00886277425577071,0.0428270863754735,3.20951415463519,1.60527496510844,6.71737424952721,0.000692182406013696,0.000408210814992248,0.00119248708177883,3.54240797176599,2.49560124043154,5.15073328448319,4.14618201517625,1.77255485115414,8.56541727509471,9.67008933239456,4.14175878637719,23.2510151673034,1.14618201517625,1.32991066760544,PCV7 +Morocco.pre.PCV,3,200,212566,1,0,1,adjusted_type_specific_negbin,0.00133541326059707,0.000156762255157922,0.00696287118803732,3.20951415463519,1.60527496510844,6.71737424952721,0.00204128172923258,0.00122747712323621,0.0034228107995988,3.54240797176599,2.49560124043154,5.15073328448319,0.267082652119414,0.0313524510315844,1.39257423760746,1.85902878612391,0.231240352943877,9.19219133184644,0.267082652119414,0.859028786123912,PCV13 +Morocco.pre.PCV,4,200,212566,1,1,0,adjusted_type_specific_negbin,0.00191745992195328,0.000228018550685366,0.00958587938973982,3.20951415463519,1.60527496510844,6.71737424952721,0.00192779838425174,0.000997131419153093,0.0037122156946575,3.54240797176599,2.49560124043154,5.15073328448319,0.383491984390656,0.0456037101370732,1.91717587794796,2.50047483161867,0.315186019413866,12.8447560195569,0.616508015609344,2.50047483161867,PCV7 +Morocco.pre.PCV,6A,200,212566,1,13,34,adjusted_type_specific_negbin,0.0759591982304262,0.0467653277202844,0.115692986662553,3.20951415463519,1.60527496510844,6.71737424952721,0.000435339407238099,0.000258206426923454,0.000737138290024887,3.54240797176599,2.49560124043154,5.15073328448319,15.1918396460852,9.35306554405688,23.1385973325105,22.3020267387362,11.7275264636134,45.8568784143171,2.19183964608524,11.6979732612638,PCV13 +Morocco.pre.PCV,6B,200,212566,1,10,21,adjusted_type_specific_negbin,0.0509091867710262,0.0280944085480349,0.0840828616170836,3.20951415463519,1.60527496510844,6.71737424952721,0.000751585706256842,0.000448497435411389,0.001258866189586,3.54240797176599,2.49560124043154,5.15073328448319,10.1818373542052,5.61888170960699,16.8165723234167,25.8410572885527,12.2343564330405,57.7100507167227,0.181837354205246,4.84105728855267,PCV7 +Morocco.pre.PCV,8,200,212566,1,1,0,adjusted_type_specific_negbin,0.00187383613286067,0.000196966552586272,0.0099114092288067,3.20951415463519,1.60527496510844,6.71737424952721,0.00192778518247364,0.000884503659754045,0.00411288030360442,3.54240797176599,2.49560124043154,5.15073328448319,0.374767226572134,0.0393933105172544,1.98228184576134,2.4520398387942,0.2847471302482,13.2752918516559,0.625232773427866,2.4520398387942,PCV20 diff --git a/examples/study_adjusted_type_specific_poisson_serotype_fit.csv b/examples/study_adjusted_type_specific_poisson_serotype_fit.csv index 57aabd1..bf63ac3 100644 --- a/examples/study_adjusted_type_specific_poisson_serotype_fit.csv +++ b/examples/study_adjusted_type_specific_poisson_serotype_fit.csv @@ -1,539 +1,539 @@ -study,type,carriage_samples,surveillance_population,time_interval,carriage,disease,model_name,rho,rho_lower,rho_upper,delta,delta_lower,delta_upper,nu,nu_lower,nu_upper,carriage_prediction,carriage_prediction_lower,carriage_prediction_upper,disease_prediction,disease_prediction_lower,disease_prediction_upper,carriage_rmse,disease_rmse,classification -Alabama.pre.PCV,1,827,19316,3.4,5,4,adjusted_type_specific_poisson,0.00426603765996625,0.00183354040966574,0.00795890355951341,1.19875580543853,0.714658830779599,1.8786251826356,0.0206062908877376,0.0133467842050282,0.0309526551119594,3.52801314479209,1.51633791879357,6.58201324371759,6.47437504318908,3.03165698122966,11.3432525999625,1.47198685520791,2.47437504318908,PCV10 -Alabama.pre.PCV,13,827,19316,3.4,6,0,adjusted_type_specific_poisson,0.00783038327991973,0.00315713133433666,0.0146255700721402,1.19875580543853,0.714658830779599,1.8786251826356,0.000869816776002311,0.000245481001501479,0.00212058387716859,6.47572697249362,2.61094761349642,12.09534644966,0.513054682937736,0.104503528601649,1.3999461163899,0.475726972493616,0.513054682937736,No PCV -Alabama.pre.PCV,14,827,19316,3.4,20,18,adjusted_type_specific_poisson,0.0322922463007771,0.022146568206295,0.0443390884796662,1.19875580543853,0.714658830779599,1.8786251826356,0.00486577684119951,0.00359593248342883,0.00641271837258626,26.7056876907426,18.3152119066059,36.668426172684,11.9907329284794,7.38168973188106,17.8696833644345,6.70568769074264,6.00926707152059,PCV7 -Alabama.pre.PCV,20,827,19316,3.4,3,0,adjusted_type_specific_poisson,0.00444757315100521,0.00120173390976518,0.00987420685224371,1.19875580543853,0.714658830779599,1.8786251826356,0.000957797173992484,0.000238388518107766,0.00247568343665466,3.67814299588131,0.993833943375806,8.16596906680555,0.319739006371189,0.047220468020034,1.01807377923931,0.678142995881312,0.319739006371189,PPV23 -Alabama.pre.PCV,3,827,19316,3.4,35,0,adjusted_type_specific_poisson,0.0364268596497743,0.0254909654725449,0.0494126721681218,1.19875580543853,0.714658830779599,1.8786251826356,0.00214630789735218,0.00150111695338643,0.00296037810122135,30.1250129303634,21.0810284457946,40.8642798830368,6.00919342334915,3.38282376714158,9.6782291659292,4.87498706963662,6.00919342334915,PCV13 -Alabama.pre.PCV,31,827,19316,3.4,0,1,adjusted_type_specific_poisson,0.00229934872082344,0.000275915461221893,0.00650757147622287,1.19875580543853,0.714658830779599,1.8786251826356,0.000529235275657269,0.000187950733188048,0.00110145716265855,1.90156139212098,0.228182086430506,5.38176161083631,0.0935429781785231,0.00803803357586795,0.320697153067124,1.90156139212098,0.906457021821477,No PCV -Alabama.pre.PCV,37,827,19316,3.4,13,0,adjusted_type_specific_poisson,0.0166537500579532,0.00912751708436922,0.0262710676793667,1.19875580543853,0.714658830779599,1.8786251826356,0.000155201681937787,5.20169758717572e-06,0.000602123592537372,13.7726512979273,7.54845662877335,21.7261729708363,0.196209436440734,0.0060728841727017,0.782607899429601,0.772651297927295,0.196209436440734,No PCV -Alabama.pre.PCV,38,827,19316,3.4,3,0,adjusted_type_specific_poisson,0.00439796684527515,0.0012114741235111,0.00967021436311002,1.19875580543853,0.714658830779599,1.8786251826356,0.00107630112860654,0.000517329118040196,0.00192400799311281,3.63711858104255,1.00188910014368,7.99726727829199,0.363225427663126,0.0785628145408326,0.957972628186196,0.63711858104255,0.363225427663126,No PCV -Alabama.pre.PCV,4,827,19316,3.4,14,8,adjusted_type_specific_poisson,0.0225073010768174,0.014176467029512,0.032825938008681,1.19875580543853,0.714658830779599,1.8786251826356,0.00249105790199758,0.00143369758150515,0.00400799422771078,18.613537990528,11.7239382334064,27.1470507331792,4.2522622304009,2.09993158651034,7.34204830261899,4.61353799052796,3.7477377695991,PCV7 -Alabama.pre.PCV,5,827,19316,3.4,0,1,adjusted_type_specific_poisson,0.00136722259935981,0.000160763680555651,0.00396449915718123,1.19875580543853,0.714658830779599,1.8786251826356,0.00898185496955944,0.00375244500011871,0.0188069207217874,1.13069308967056,0.132951563819524,3.27864080298887,0.869902446702919,0.0966662769388696,2.61344762898449,1.13069308967056,0.130097553297081,PCV10 -Alabama.pre.PCV,8,827,19316,3.4,4,0,adjusted_type_specific_poisson,0.00493047853554577,0.00155806534646385,0.0101509325876282,1.19875580543853,0.714658830779599,1.8786251826356,0.00244545634969096,0.00123914949735586,0.00432306004960451,4.07750574889635,1.28852004152561,8.39482124996853,0.914491399875437,0.240976831808842,2.18381895663266,0.0775057488963542,0.914491399875437,PCV20 -Barcelona.post.PCV7,1,209,228000,4,2,39,adjusted_type_specific_poisson,0.0154743206128811,0.00873485792479642,0.0248949621822575,0.141537337843307,0.100972879471476,0.193782719189535,0.0206062908877376,0.0133467842050282,0.0309526551119594,3.23413300809215,1.82558530628245,5.20304709609183,38.7593470427124,27.8626970226784,51.2473497296823,1.23413300809215,0.240652957287566,PCV10 -Barcelona.post.PCV7,10A,209,228000,4,10,2,adjusted_type_specific_poisson,0.0421487454367268,0.0222792842427902,0.0684947234360143,0.141537337843307,0.100972879471476,0.193782719189535,0.000793695374669934,0.000513989148006867,0.00115253233769801,8.80908779627589,4.65637040674315,14.315397198127,4.205968807227,2.0996293526796,7.16822250351363,1.19091220372411,2.205968807227,PCV20 -Barcelona.post.PCV7,11A,209,228000,4,9,0,adjusted_type_specific_poisson,0.0453122955031539,0.0221258722285897,0.0757361628376527,0.141537337843307,0.100972879471476,0.193782719189535,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,9.47026976015916,4.62430729577524,15.8288580330694,0.493237304488938,0.179811809450915,1.01874715721755,0.470269760159162,0.493237304488938,PCV20 -Barcelona.post.PCV7,14,209,228000,4,4,6,adjusted_type_specific_poisson,0.0134532164887539,0.00643694415404851,0.0234695096977265,0.141537337843307,0.100972879471476,0.193782719189535,0.00486577684119951,0.00359593248342883,0.00641271837258626,2.81172224614956,1.34532132819614,4.90512752682484,8.18862643197313,4.09457651186451,13.6372205927039,1.18827775385044,2.18862643197313,PCV7 -Barcelona.post.PCV7,15A,209,228000,4,6,2,adjusted_type_specific_poisson,0.0336956443150179,0.0155580023204583,0.0589594859765825,0.141537337843307,0.100972879471476,0.193782719189535,0.000447893348168094,0.000276077603700969,0.000677854020290881,7.04238966183874,3.25162248497578,12.3225325691057,1.90524011120224,0.791091453277429,3.64938223777768,1.04238966183874,0.0947598887977603,No PCV -Barcelona.post.PCV7,15B/C,209,228000,4,13,3,adjusted_type_specific_poisson,0.0647880480518996,0.03812189287282,0.0985588908395898,0.141537337843307,0.100972879471476,0.193782719189535,0.000410284575081173,0.000285934443755961,0.000563977573171364,13.540702042847,7.96747561041939,20.5988081854743,3.37035096200927,1.82719375449366,5.55124047735356,0.540702042847013,0.370350962009266,PCV20 -Barcelona.post.PCV7,16F,209,228000,4,5,2,adjusted_type_specific_poisson,0.0299397559225836,0.0129406185670591,0.0538823590490838,0.141537337843307,0.100972879471476,0.193782719189535,0.000442387133406364,0.000231326668676358,0.000740352472096137,6.25740898781996,2.70458928051536,11.2614130412585,1.66011037705037,0.61169842633106,3.38663264148028,1.25740898781996,0.339889622949628,No PCV -Barcelona.post.PCV7,17F,209,228000,4,5,0,adjusted_type_specific_poisson,0.023035175820704,0.00851792596890626,0.0443878297836701,0.141537337843307,0.100972879471476,0.193782719189535,0.000400957354522875,0.000201346292292629,0.000689191021815353,4.81435174652714,1.78024652750141,9.27705642478706,1.15694092228221,0.359172643576867,2.52943557285651,0.185648253472864,1.15694092228221,PPV23 -Barcelona.post.PCV7,19A,209,228000,4,21,34,adjusted_type_specific_poisson,0.121981957064761,0.0891111369417886,0.159903852605657,0.141537337843307,0.100972879471476,0.193782719189535,0.00193665997116141,0.00151058619668583,0.00243196471893208,25.494229026535,18.6242276208338,33.4199051945823,29.8458939697672,21.9099029613504,39.1464268308427,4.49422902653496,4.15410603023285,PCV13 -Barcelona.post.PCV7,19F,209,228000,4,13,7,adjusted_type_specific_poisson,0.0684630329912845,0.042128984984159,0.101071565448226,0.141537337843307,0.100972879471476,0.193782719189535,0.000752568056083617,0.000550123319373138,0.00100157805364369,14.3087738951785,8.80495786168924,21.1239571786792,6.52073861977365,3.81784566062591,10.0935557914445,1.30877389517846,0.479261380226354,PCV7 -Barcelona.post.PCV7,21,209,228000,4,5,0,adjusted_type_specific_poisson,0.0250167938670911,0.00923675998544921,0.048463615225411,0.141537337843307,0.100972879471476,0.193782719189535,0.000234606065585659,0.00010602199615295,0.000423079520489989,5.22850991822203,1.93048283695889,10.1288955821109,0.738446893527389,0.21342043587164,1.70856863617167,0.228509918222034,0.738446893527389,No PCV -Barcelona.post.PCV7,22F,209,228000,4,8,3,adjusted_type_specific_poisson,0.0344708536028072,0.0174704192549739,0.0575760011642648,0.141537337843307,0.100972879471476,0.193782719189535,0.00111291794656347,0.000747288532056908,0.00157611065350571,7.2044084029867,3.65131762428955,12.0333842433313,4.81704784233454,2.36051657969564,8.23275223890294,0.795591597013301,1.81704784233454,PCV15 -Barcelona.post.PCV7,23A,209,228000,4,9,0,adjusted_type_specific_poisson,0.042971580363064,0.0204493419710399,0.0731732457511488,0.141537337843307,0.100972879471476,0.193782719189535,0.00017858253466746,0.000100358645533425,0.000284446850590249,8.98106029588038,4.27391247194733,15.2932083619901,0.973127891727234,0.387750132950331,1.92275331719251,0.0189397041196155,0.973127891727234,No PCV -Barcelona.post.PCV7,23B,209,228000,4,17,5,adjusted_type_specific_poisson,0.0922493902076685,0.0589784575531371,0.132089258495159,0.141537337843307,0.100972879471476,0.193782719189535,0.000290469676688038,0.000174295346379655,0.000444118199022155,19.2801225534027,12.3264976286057,27.6066550254883,3.38827842316114,1.78533305102277,5.63648802224179,2.28012255340272,1.61172157683886,No PCV -Barcelona.post.PCV7,23F,209,228000,4,7,4,adjusted_type_specific_poisson,0.0388119155265761,0.0199731272021361,0.0641130404857854,0.141537337843307,0.100972879471476,0.193782719189535,0.00077564137009531,0.000556479798610777,0.00105106918760042,8.1116903450544,4.17438358524645,13.3996254615291,3.80528773687339,1.87048535510154,6.50054074485778,1.1116903450544,0.194712263126613,PCV7 -Barcelona.post.PCV7,3,209,228000,4,2,8,adjusted_type_specific_poisson,0.0228637135059625,0.0108774885059568,0.0398627547188156,0.141537337843307,0.100972879471476,0.193782719189535,0.00214630789735218,0.00150111695338643,0.00296037810122135,4.77851612274616,2.27339509774497,8.33131573623246,6.13903781417472,2.9636173087983,10.5540376992936,2.77851612274616,1.86096218582528,PCV13 -Barcelona.post.PCV7,34,209,228000,4,6,0,adjusted_type_specific_poisson,0.0311365457862869,0.0127537456774768,0.0575053584497326,0.141537337843307,0.100972879471476,0.193782719189535,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,6.50753806933395,2.66553284659266,12.0186199159941,0.458747911613734,0.0732760328664659,1.29570993195922,0.507538069333952,0.458747911613734,No PCV -Barcelona.post.PCV7,35B,209,228000,4,5,0,adjusted_type_specific_poisson,0.0262208274822598,0.00982981652898998,0.0501807707724591,0.141537337843307,0.100972879471476,0.193782719189535,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,5.48015294379229,2.05443165455891,10.4877810914439,0.479019257660756,0.141524225041597,1.09667464026793,0.480152943792287,0.479019257660756,No PCV -Barcelona.post.PCV7,5,209,228000,4,0,14,adjusted_type_specific_poisson,0.0123928078839717,0.0047040585018329,0.0250117827198176,0.141537337843307,0.100972879471476,0.193782719189535,0.00898185496955944,0.00375244500011871,0.0188069207217874,2.59009684775008,0.983148226883076,5.22746258844188,12.3339459299745,6.77895558026578,19.6282761683322,2.59009684775008,1.66605407002545,PCV10 -Barcelona.post.PCV7,6A,209,228000,4,16,4,adjusted_type_specific_poisson,0.0777531220794832,0.0483439941843233,0.113536812929762,0.141537337843307,0.100972879471476,0.193782719189535,0.000470534749603847,0.000335293276070173,0.000638312814574088,16.250402514612,10.1038947845236,23.7291939023203,4.63657769965564,2.65385995088009,7.29568327609223,0.250402514611991,0.636577699655636,PCV13 -Barcelona.post.PCV7,6B,209,228000,4,4,2,adjusted_type_specific_poisson,0.0226878460300497,0.00926603044038105,0.0419777169759067,0.141537337843307,0.100972879471476,0.193782719189535,0.000770579380902745,0.000565085521465747,0.00101866271810419,4.74175982028038,1.93660036203964,8.77334284796449,2.21330809275599,0.878675731289215,4.23582843235617,0.741759820280382,0.213308092755995,PCV7 -Barcelona.post.PCV7,6C,209,228000,4,19,1,adjusted_type_specific_poisson,0.0939719898429331,0.0596393320765304,0.13594906191611,0.141537337843307,0.100972879471476,0.193782719189535,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,19.640145877173,12.4646204039949,28.413353940467,1.21652880137937,0.46521526602959,2.4253399903607,0.640145877173019,0.216528801379368,No PCV -Barcelona.post.PCV7,7F,209,228000,4,0,14,adjusted_type_specific_poisson,0.0104351250135082,0.00511175037093656,0.0182214410864372,0.141537337843307,0.100972879471476,0.193782719189535,0.00997721126084835,0.00681051079664878,0.01416409744657,2.18094112782322,1.06835582752574,3.80828118706537,12.8221234179997,7.08515244665701,20.4090453931105,2.18094112782322,1.17787658200031,PCV10 -Bogota.post.PCV7,1,246,357200,1,0,8,adjusted_type_specific_poisson,0.00218096456402636,0.000836002386059073,0.00440549512875176,0.568782436950064,0.371915703745803,0.83467097324259,0.0206062908877376,0.0133467842050282,0.0309526551119594,0.536517282750485,0.205656586970532,1.08375180167293,8.46087311960381,3.88568480540506,14.7352455854403,0.536517282750485,0.460873119603812,PCV10 -Bogota.post.PCV7,10A,246,357200,1,1,0,adjusted_type_specific_poisson,0.00496991858909226,0.000600696234017059,0.0140453198097712,0.568782436950064,0.371915703745803,0.83467097324259,0.000793695374669934,0.000513989148006867,0.00115253233769801,1.2225999729167,0.147771273568197,3.45514867320373,0.774279082697746,0.0926610764897658,2.22001819420439,0.222599972916696,0.774279082697746,PCV20 -Bogota.post.PCV7,11A,246,357200,1,7,2,adjusted_type_specific_poisson,0.0375357961962462,0.0183422378741341,0.0632414180128009,0.568782436950064,0.371915703745803,0.83467097324259,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,9.23380586427657,4.51219051703698,15.557388831149,0.641296022836896,0.226256716716028,1.36412215717718,2.23380586427657,1.3587039771631,PCV20 -Bogota.post.PCV7,13,246,357200,1,1,0,adjusted_type_specific_poisson,0.00496244787019975,0.000559245594334129,0.014473970366392,0.568782436950064,0.371915703745803,0.83467097324259,0.000869816776002311,0.000245481001501479,0.00212058387716859,1.22076217606914,0.137574416206196,3.56059671013244,0.76574309522728,0.0814250815932786,2.40378029661226,0.220762176069138,0.76574309522728,No PCV -Bogota.post.PCV7,14,246,357200,1,3,14,adjusted_type_specific_poisson,0.015051029276029,0.00800127766860833,0.0247957497393835,0.568782436950064,0.371915703745803,0.83467097324259,0.00486577684119951,0.00359593248342883,0.00641271837258626,3.70255320190314,1.96831430647765,6.09975443588834,14.2484475487213,8.33560230680877,21.7219556905116,0.702553201903145,0.248447548721265,PCV7 -Bogota.post.PCV7,15A,246,357200,1,2,2,adjusted_type_specific_poisson,0.0147799224165673,0.00472267081681633,0.030579814235718,0.568782436950064,0.371915703745803,0.83467097324259,0.000447893348168094,0.000276077603700969,0.000677854020290881,3.63586091447555,1.16177702093682,7.52263430198663,1.30745847972699,0.387837180742623,2.88721723924349,1.63586091447555,0.692541520273011,No PCV -Bogota.post.PCV7,15B/C,246,357200,1,13,5,adjusted_type_specific_poisson,0.0576084423254213,0.0344605894511129,0.0863173085318511,0.568782436950064,0.371915703745803,0.83467097324259,0.000410284575081173,0.000285934443755961,0.000563977573171364,14.1716768120536,8.47730500497378,21.2340578988354,4.68687328902712,2.54695030306283,7.58296110301353,1.17167681205364,0.31312671097288,PCV20 -Bogota.post.PCV7,16F,246,357200,1,1,2,adjusted_type_specific_poisson,0.0119053411165273,0.00319370557194122,0.026367175261888,0.568782436950064,0.371915703745803,0.83467097324259,0.000442387133406364,0.000231326668676358,0.000740352472096137,2.92871391466573,0.78565157069754,6.48632511442446,1.03026095441067,0.242090410341213,2.4893181893518,1.92871391466573,0.969739045589334,No PCV -Bogota.post.PCV7,17F,246,357200,1,2,0,adjusted_type_specific_poisson,0.00921235672946678,0.00187554225353834,0.0222291928600805,0.568782436950064,0.371915703745803,0.83467097324259,0.000400957354522875,0.000201346292292629,0.000689191021815353,2.26623975544883,0.461383394370431,5.4683814435798,0.723897762711897,0.131815127545162,1.9011164871927,0.266239755448828,0.723897762711897,PPV23 -Bogota.post.PCV7,18A,246,357200,1,1,0,adjusted_type_specific_poisson,0.0066803487397296,0.000791280360283161,0.0188329457003582,0.568782436950064,0.371915703745803,0.83467097324259,0.000283343585215039,2.68111527639592e-05,0.000946066820544266,1.64336578997348,0.194654968629658,4.63290464228813,0.334571473891824,0.0168081077286764,1.29641835123484,0.643365789973482,0.334571473891824,No PCV -Bogota.post.PCV7,18C,246,357200,1,2,5,adjusted_type_specific_poisson,0.00889668149272721,0.00347448746476051,0.017288816114225,0.568782436950064,0.371915703745803,0.83467097324259,0.00341462550925104,0.0021814214974022,0.00511035484325696,2.18858364721089,0.854723916331087,4.25304876409935,5.81446063465911,2.46491513578983,10.5363218687208,0.188583647210894,0.814460634659114,PCV7 -Bogota.post.PCV7,19A,246,357200,1,3,5,adjusted_type_specific_poisson,0.0143190340106413,0.00628810176753245,0.0258258081315226,0.568782436950064,0.371915703745803,0.83467097324259,0.00193665997116141,0.00151058619668583,0.00243196471893208,3.52248236661776,1.54687303481298,6.35314880035456,5.45535890161859,2.44466772941186,9.70757195351835,0.522482366617765,0.455358901618591,PCV13 -Bogota.post.PCV7,19B,246,357200,1,1,0,adjusted_type_specific_poisson,0.0077935995399745,0.000949803110828954,0.0215612454178215,0.568782436950064,0.371915703745803,0.83467097324259,5.9946555297865e-05,1.12624360826675e-06,0.00041337033542345,1.91722548683373,0.233651565263923,5.3040663727841,0.075798425331988,0.000663819668061402,0.556004887068916,0.917225486833727,0.075798425331988,No PCV -Bogota.post.PCV7,19F,246,357200,1,3,2,adjusted_type_specific_poisson,0.0151819796219858,0.00549373244066758,0.0298487528755177,0.568782436950064,0.371915703745803,0.83467097324259,0.000752568056083617,0.000550123319373138,0.00100157805364369,3.7347669870085,1.35145818040422,7.34279320737736,2.25840048687437,0.795051292448175,4.57974792817381,0.734766987008497,0.258400486874371,PCV7 -Bogota.post.PCV7,20,246,357200,1,0,1,adjusted_type_specific_poisson,0.00483178787274011,0.00053568368392145,0.0142383294175378,0.568782436950064,0.371915703745803,0.83467097324259,0.000957797173992484,0.000238388518107766,0.00247568343665466,1.18861981669407,0.131778186244677,3.50262903671431,0.80766093269,0.0774930355847006,2.56566022651211,1.18861981669407,0.19233906731,PPV23 -Bogota.post.PCV7,22F,246,357200,1,0,1,adjusted_type_specific_poisson,0.00428214719752991,0.000508056112699302,0.0121819235627085,0.568782436950064,0.371915703745803,0.83467097324259,0.00111291794656347,0.000747288532056908,0.00157611065350571,1.05340821059236,0.124981803724028,2.99675319642629,0.934488891860294,0.109910737655176,2.69700651752595,1.05340821059236,0.0655111081397055,PCV15 -Bogota.post.PCV7,23A,246,357200,1,6,0,adjusted_type_specific_poisson,0.0247974276199383,0.0100818888482071,0.046361639513407,0.568782436950064,0.371915703745803,0.83467097324259,0.00017858253466746,0.000100358645533425,0.000284446850590249,6.10016719450482,2.48014465665895,11.4049633202981,0.88040586328587,0.301485202854151,1.87802147485684,0.100167194504824,0.88040586328587,No PCV -Bogota.post.PCV7,23B,246,357200,1,1,1,adjusted_type_specific_poisson,0.0097842916271618,0.00199528571782327,0.0235293139730909,0.568782436950064,0.371915703745803,0.83467097324259,0.000290469676688038,0.000174295346379655,0.000444118199022155,2.4069357402818,0.490840286584525,5.78821123738037,0.562370872019717,0.103625876248888,1.43795482216085,1.4069357402818,0.437629127980283,No PCV -Bogota.post.PCV7,23F,246,357200,1,5,4,adjusted_type_specific_poisson,0.0249420568466068,0.0117305400166249,0.0432025071543331,0.568782436950064,0.371915703745803,0.83467097324259,0.00077564137009531,0.000556479798610777,0.00105106918760042,6.13574598426527,2.88571284408972,10.6278167599659,3.81713513685224,1.74487053724181,6.82494312274104,1.13574598426527,0.182864863147762,PCV7 -Bogota.post.PCV7,24F,246,357200,1,1,1,adjusted_type_specific_poisson,0.00371685148592932,0.000716842594039145,0.00954399214895464,0.568782436950064,0.371915703745803,0.83467097324259,0.00296592942741409,0.00168198604203905,0.00494246465975427,0.914345465538613,0.17634327813363,2.34782206864284,2.07602391544006,0.421928561384929,5.07714722989282,0.085654534461387,1.07602391544006,No PCV -Bogota.post.PCV7,25A,246,357200,1,0,3,adjusted_type_specific_poisson,0.00653208227010543,0.00154877851281112,0.0159788403033555,0.568782436950064,0.371915703745803,0.83467097324259,0.00205858895387132,0.0008321684683761,0.00449630852733197,1.60689223844594,0.380999514151535,3.93079471462546,2.38944408938752,0.614882092735826,5.46192847581974,1.60689223844594,0.610555910612478,No PCV -Bogota.post.PCV7,28A,246,357200,1,0,2,adjusted_type_specific_poisson,0.00409072631064496,0.000105775596802769,0.0151189732380204,0.568782436950064,0.371915703745803,0.83467097324259,0.0159509431263682,0.000214486677653748,0.0981163999297224,1.00631867241866,0.0260207968134812,3.71926741655302,2.00792032618622,0.239570152386603,5.67636717844267,1.00631867241866,0.00792032618622196,No PCV -Bogota.post.PCV7,29,246,357200,1,1,0,adjusted_type_specific_poisson,0.00748588239815484,0.000887406940990178,0.0210158345191338,0.568782436950064,0.371915703745803,0.83467097324259,0.000105704622446372,3.26554376138359e-06,0.000442922821034247,1.84152706994609,0.218302107483584,5.16989529170691,0.144961140106378,0.00261669160716782,0.702317391640031,0.84152706994609,0.144961140106378,No PCV -Bogota.post.PCV7,3,246,357200,1,1,12,adjusted_type_specific_poisson,0.0209030922041616,0.0107501120778345,0.0349339400254774,0.568782436950064,0.371915703745803,0.83467097324259,0.00214630789735218,0.00150111695338643,0.00296037810122135,5.14216068222375,2.64452757114729,8.59374924626745,8.7486587020481,4.65633360147759,14.1462733619784,4.14216068222375,3.2513412979519,PCV13 -Bogota.post.PCV7,35B,246,357200,1,5,2,adjusted_type_specific_poisson,0.0287300502472624,0.0125112637054963,0.0514942344735539,0.568782436950064,0.371915703745803,0.83467097324259,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,7.06759236082656,3.07777087155209,12.6675816804943,0.821822262825113,0.267470382234565,1.81227693737134,2.06759236082656,1.17817773717489,No PCV -Bogota.post.PCV7,35F,246,357200,1,3,0,adjusted_type_specific_poisson,0.0140411776055517,0.00379068767193296,0.0306248486656995,0.568782436950064,0.371915703745803,0.83467097324259,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,3.45412969096573,0.932509167295509,7.53371277176208,0.504009697206256,0.112185709546592,1.26754693641635,0.454129690965725,0.504009697206256,No PCV -Bogota.post.PCV7,4,246,357200,1,0,1,adjusted_type_specific_poisson,0.00279112051938471,0.000317533719401215,0.00820510594420782,0.568782436950064,0.371915703745803,0.83467097324259,0.00249105790199758,0.00143369758150515,0.00400799422771078,0.686615647768638,0.078113294972699,2.01845606227512,1.31999057684477,0.1537252519555,3.76916623103435,0.686615647768638,0.319990576844768,PCV7 -Bogota.post.PCV7,42,246,357200,1,1,0,adjusted_type_specific_poisson,0.00761437627912596,0.00089127496445367,0.0215329530832475,0.568782436950064,0.371915703745803,0.83467097324259,0.000106976485278402,1.13850123454097e-06,0.000791514809070834,1.87313656466499,0.219253641255603,5.29710645847887,0.118287800081757,0.00071708692577598,0.869137120979815,0.873136564664986,0.118287800081757,No PCV -Bogota.post.PCV7,5,246,357200,1,0,1,adjusted_type_specific_poisson,0.00111821843343572,0.000110561641016317,0.0035879585905003,0.568782436950064,0.371915703745803,0.83467097324259,0.00898185496955944,0.00375244500011871,0.0188069207217874,0.275081734625188,0.0271981636900139,0.882637813263075,1.71704803960185,0.198068237582898,4.83823516707308,0.275081734625188,0.717048039601846,PCV10 -Bogota.post.PCV7,6A,246,357200,1,6,1,adjusted_type_specific_poisson,0.0235740144797875,0.0102443872585304,0.0422875741505731,0.568782436950064,0.371915703745803,0.83467097324259,0.000470534749603847,0.000335293276070173,0.000638312814574088,5.79920756202774,2.52011926559847,10.402743241041,2.20041973946568,0.903485631411004,4.21555020835303,0.200792437972265,1.20041973946568,PCV13 -Bogota.post.PCV7,6B,246,357200,1,2,4,adjusted_type_specific_poisson,0.0174392718149102,0.00695621362175725,0.0327623558103668,0.568782436950064,0.371915703745803,0.83467097324259,0.000770579380902745,0.000565085521465747,0.00101866271810419,4.2900608664679,1.71122855095228,8.05953952935022,2.65528698422736,1.05113301707969,5.10097293159367,2.2900608664679,1.34471301577264,PCV7 -Bogota.post.PCV7,6C,246,357200,1,2,0,adjusted_type_specific_poisson,0.0112125180528908,0.00229662444978172,0.0268984134036901,0.568782436950064,0.371915703745803,0.83467097324259,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,2.75827944101115,0.564969614646303,6.61700969730778,0.227575107280488,0.0359123901197473,0.646986473147226,0.758279441011147,0.227575107280488,No PCV -Bogota.post.PCV7,7C,246,357200,1,1,0,adjusted_type_specific_poisson,0.00610743912561715,0.000746458251724225,0.0171983017050802,0.568782436950064,0.371915703745803,0.83467097324259,0.000430538003690001,0.000121592824190092,0.000973102091763221,1.50243002490182,0.183628729924159,4.23078221944974,0.4953023094131,0.0463116338444934,1.58704945731415,0.50243002490182,0.4953023094131,No PCV -Bogota.post.PCV7,8,246,357200,1,0,2,adjusted_type_specific_poisson,0.00426712750140937,0.00081249159071454,0.0108444476107507,0.568782436950064,0.371915703745803,0.83467097324259,0.00244545634969096,0.00123914949735586,0.00432306004960451,1.0497133653467,0.199872931315777,2.66773411224467,1.94067030840493,0.390639944626958,4.7112492736076,1.0497133653467,0.0593296915950721,PCV20 -Bogota.post.PCV7,9V,246,357200,1,0,2,adjusted_type_specific_poisson,0.00404162251921212,0.000819362451401086,0.0101816787801985,0.568782436950064,0.371915703745803,0.83467097324259,0.00259101673359874,0.00162148522659737,0.00391316735192488,0.99423913972618,0.201563163044667,2.50469297992883,2.00583288879994,0.422028961773515,4.85625803082803,0.99423913972618,0.00583288879993971,PCV7 -Bogota.pre.PCV,1,197,357200,4,0,29,adjusted_type_specific_poisson,0.00491619784596717,0.00262947340511251,0.00823888577174459,0.213075270335225,0.153528489818432,0.28922843608303,0.0206062908877376,0.0133467842050282,0.0309526551119594,0.968490975655533,0.518006260807165,1.62306049703368,29.0022232762062,19.6562427225869,40.2165078260121,0.968490975655533,0.00222327620620533,PCV10 -Bogota.pre.PCV,10A,197,357200,4,3,1,adjusted_type_specific_poisson,0.0116303725480437,0.0036893478577599,0.0244067655419521,0.213075270335225,0.153528489818432,0.28922843608303,0.000793695374669934,0.000513989148006867,0.00115253233769801,2.2911833919646,0.7268015279787,4.80813281176456,2.71088224881148,0.867798337965515,5.64984359240543,0.708816608035397,1.71088224881148,PCV20 -Bogota.pre.PCV,10B,197,357200,4,0,1,adjusted_type_specific_poisson,0.00557223606139305,0.000549962904697589,0.017177791744628,0.213075270335225,0.153528489818432,0.28922843608303,0.000696632980137251,9.61989918783685e-05,0.00234483425439832,1.09773050409443,0.108342692225425,3.38402497369172,0.885418059023909,0.0752275181099545,2.88348913214837,1.09773050409443,0.114581940976091,No PCV -Bogota.pre.PCV,11A,197,357200,4,4,1,adjusted_type_specific_poisson,0.026710317949857,0.00977233221999761,0.0514673030197689,0.213075270335225,0.153528489818432,0.28922843608303,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,5.26193263612184,1.92514944733953,10.1390586948945,0.681377422245352,0.203598303312064,1.53396509621344,1.26193263612184,0.318622577754648,PCV20 -Bogota.pre.PCV,12F,197,357200,4,0,3,adjusted_type_specific_poisson,0.00173777335172704,0.000399058458800367,0.00436488914694793,0.213075270335225,0.153528489818432,0.28922843608303,0.00763701563010158,0.00413184393687895,0.0128667210227945,0.342341350290226,0.0786145163836722,0.859883161948742,3.66548363112729,1.00173198160956,8.01493135104405,0.342341350290226,0.665483631127289,PCV20 -Bogota.pre.PCV,13,197,357200,4,1,4,adjusted_type_specific_poisson,0.0141580043055005,0.00423772083044901,0.0313969774599614,0.213075270335225,0.153528489818432,0.28922843608303,0.000869816776002311,0.000245481001501479,0.00212058387716859,2.78912684818359,0.834831003598454,6.1852045596124,3.17174109371145,0.965805837679133,6.82957353949471,1.78912684818359,0.828258906288551,No PCV -Bogota.pre.PCV,14,197,357200,4,9,163,adjusted_type_specific_poisson,0.10499181914019,0.07872399244181,0.135237036791282,0.213075270335225,0.153528489818432,0.28922843608303,0.00486577684119951,0.00359593248342883,0.00641271837258626,20.6833883706174,15.5086265110366,26.6416962478826,150.903623751889,128.677757161579,174.562041057168,11.6833883706174,12.0963762481109,PCV7 -Bogota.pre.PCV,15A,197,357200,4,0,1,adjusted_type_specific_poisson,0.00604402224290473,0.000727527091773201,0.0168291913674287,0.213075270335225,0.153528489818432,0.28922843608303,0.000447893348168094,0.000276077603700969,0.000677854020290881,1.19067238185223,0.143322837079321,3.31535069938346,0.798135423979664,0.0953287219556345,2.25547777893869,1.19067238185223,0.201864576020336,No PCV -Bogota.pre.PCV,15B/C,197,357200,4,6,2,adjusted_type_specific_poisson,0.0281756909837361,0.0127520184677747,0.0493797427347474,0.213075270335225,0.153528489818432,0.28922843608303,0.000410284575081173,0.000285934443755961,0.000563977573171364,5.55061112379602,2.51214763815162,9.72780931874525,3.43783943052147,1.52512257576388,6.22844768363695,0.449388876203979,1.43783943052147,PCV20 -Bogota.pre.PCV,15F,197,357200,4,1,0,adjusted_type_specific_poisson,0.00766757438043841,0.000906991143193494,0.0218649372472944,0.213075270335225,0.153528489818432,0.28922843608303,0.000241837303648991,2.36364376734738e-05,0.000792155722410316,1.51051215294637,0.178677255209118,4.30739263771699,0.475502840975461,0.0268041942970242,1.77341097778573,0.510512152946367,0.475502840975461,No PCV -Bogota.pre.PCV,16F,197,357200,4,1,3,adjusted_type_specific_poisson,0.01523019295057,0.00470424627617887,0.0321570351125747,0.213075270335225,0.153528489818432,0.28922843608303,0.000442387133406364,0.000231326668676358,0.000740352472096137,3.0003480112623,0.926736516407238,6.33493591717722,1.95504610571179,0.580658107682881,4.21146623084765,2.0003480112623,1.04495389428821,No PCV -Bogota.pre.PCV,18A,197,357200,4,1,1,adjusted_type_specific_poisson,0.0110824228884839,0.00207072452784674,0.0279628621013383,0.213075270335225,0.153528489818432,0.28922843608303,0.000283343585215039,2.68111527639592e-05,0.000946066820544266,2.18323730903132,0.407932731985807,5.50868383396365,0.794829836285713,0.06644532232367,2.62451030019873,1.18323730903132,0.205170163714287,No PCV -Bogota.pre.PCV,18B,197,357200,4,0,1,adjusted_type_specific_poisson,0.00351463430538012,0.000297812858742935,0.0116787065138645,0.213075270335225,0.153528489818432,0.28922843608303,0.00173622469177418,0.00030591934704866,0.00552384967796135,0.692382958159883,0.0586691331723583,2.30070518323131,1.30953073192373,0.137763326746146,3.91435217594486,0.692382958159883,0.309530731923731,No PCV -Bogota.pre.PCV,18C,197,357200,4,3,11,adjusted_type_specific_poisson,0.012651108442888,0.006245365399984,0.0218375741027304,0.213075270335225,0.153528489818432,0.28922843608303,0.00341462550925104,0.0021814214974022,0.00511035484325696,2.49226836324895,1.23033698379685,4.30200209823788,12.4899494697678,6.89239942409325,19.5977900546465,0.507731636751055,1.48994946976781,PCV7 -Bogota.pre.PCV,18F,197,357200,4,0,2,adjusted_type_specific_poisson,0.0072378972832743,0.000786668237375171,0.021735619551031,0.213075270335225,0.153528489818432,0.28922843608303,0.00126829626653312,7.78271438048081e-05,0.00564867594935307,1.42586576480504,0.154973642762909,4.2819170515531,1.5638185451365,0.166011612352781,4.57509918663306,1.42586576480504,0.4361814548635,No PCV -Bogota.pre.PCV,19A,197,357200,4,3,10,adjusted_type_specific_poisson,0.0181119113177714,0.00950357869755766,0.0295537850634042,0.213075270335225,0.153528489818432,0.28922843608303,0.00193665997116141,0.00151058619668583,0.00243196471893208,3.56804652960097,1.87220500341886,5.82209565749063,10.4125457848874,5.72170156872235,16.5175397080652,0.568046529600968,0.41254578488736,PCV13 -Bogota.pre.PCV,19B,197,357200,4,1,0,adjusted_type_specific_poisson,0.00942591076339029,0.00111443578668649,0.0264571245336493,0.213075270335225,0.153528489818432,0.28922843608303,5.9946555297865e-05,1.12624360826675e-06,0.00041337033542345,1.85690442038789,0.219543849977239,5.2120535331289,0.125652612451093,0.00123641520606129,0.894397693052493,0.856904420387887,0.125652612451093,No PCV -Bogota.pre.PCV,19F,197,357200,4,25,13,adjusted_type_specific_poisson,0.0942686974887553,0.0647475017838978,0.129268564946849,0.213075270335225,0.153528489818432,0.28922843608303,0.000752568056083617,0.000550123319373138,0.00100157805364369,18.5709334052848,12.7552578514279,25.4659072945293,21.0592735177372,14.5645550996272,28.8043756552046,6.4290665947152,8.05927351773721,PCV7 -Bogota.pre.PCV,22F,197,357200,4,0,2,adjusted_type_specific_poisson,0.00573227383710077,0.00114705979772933,0.0143928644554822,0.213075270335225,0.153528489818432,0.28922843608303,0.00111291794656347,0.000747288532056908,0.00157611065350571,1.12925794590885,0.225970780152677,2.83539429772999,1.87299137220258,0.3882106319331,4.58892462805768,1.12925794590885,0.127008627797419,PCV15 -Bogota.pre.PCV,23A,197,357200,4,5,2,adjusted_type_specific_poisson,0.0316534990621275,0.0137325424620185,0.056877273967043,0.213075270335225,0.153528489818432,0.28922843608303,0.00017858253466746,0.000100358645533425,0.000284446850590249,6.23573931523911,2.70531086501764,11.2048229715075,1.67559668111995,0.647731036987963,3.31926761803326,1.23573931523911,0.324403318880046,No PCV -Bogota.pre.PCV,23B,197,357200,4,2,1,adjusted_type_specific_poisson,0.014048754711801,0.00386444117106913,0.0309309234253683,0.213075270335225,0.153528489818432,0.28922843608303,0.000290469676688038,0.000174295346379655,0.000444118199022155,2.7676046782248,0.761294910700618,6.09339191479756,1.20672222233902,0.316309667656644,2.76292950314213,0.767604678224798,0.206722222339017,No PCV -Bogota.pre.PCV,23F,197,357200,4,7,9,adjusted_type_specific_poisson,0.0395642733484249,0.0227317338688052,0.0611510480272357,0.213075270335225,0.153528489818432,0.28922843608303,0.00077564137009531,0.000556479798610777,0.00105106918760042,7.79416184963971,4.47815157215463,12.0467564613654,9.10289006420895,5.23820461724065,14.0900963223256,0.794161849639706,0.102890064208948,PCV7 -Bogota.pre.PCV,24F,197,357200,4,0,2,adjusted_type_specific_poisson,0.00289243422722206,0.000551846127909159,0.00749947632144815,0.213075270335225,0.153528489818432,0.28922843608303,0.00296592942741409,0.00168198604203905,0.00494246465975427,0.569809542762745,0.108713687198104,1.47739683532529,2.42326184475011,0.503394748606163,5.83013949925766,0.569809542762745,0.423261844750108,No PCV -Bogota.pre.PCV,25A,197,357200,4,1,2,adjusted_type_specific_poisson,0.00544188900368435,0.00119270798482569,0.013715193001157,0.213075270335225,0.153528489818432,0.28922843608303,0.00205858895387132,0.0008321684683761,0.00449630852733197,1.07205213372582,0.234963473010662,2.70189302122792,2.93496986703489,0.772993928219062,6.62992622321343,0.0720521337258166,0.934969867034895,No PCV -Bogota.pre.PCV,3,197,357200,4,1,6,adjusted_type_specific_poisson,0.00962886765736876,0.00393370678087363,0.0182393948527896,0.213075270335225,0.153528489818432,0.28922843608303,0.00214630789735218,0.00150111695338643,0.00296037810122135,1.89688692850165,0.774940235832104,3.59316078599955,6.06242051581335,2.59926721991363,10.9252154600432,0.896886928501647,0.0624205158133488,PCV13 -Bogota.pre.PCV,34,197,357200,4,3,0,adjusted_type_specific_poisson,0.0172448530674525,0.00463052668117331,0.0376490982372257,0.213075270335225,0.153528489818432,0.28922843608303,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,3.39723605428814,0.912213756191143,7.41687235273346,0.581053221077214,0.0818443469286752,1.69939507319916,0.397236054288137,0.581053221077214,No PCV -Bogota.pre.PCV,35C,197,357200,4,0,1,adjusted_type_specific_poisson,0.0050311186396846,0.000138955028571207,0.018283836088283,0.213075270335225,0.153528489818432,0.28922843608303,0.0051742628337998,1.64545998659345e-05,0.0243938191472805,0.991130372017866,0.0273741406285277,3.60191570939176,0.988572615338595,0.0247564557182165,3.61087516054942,0.991130372017866,0.0114273846614046,No PCV -Bogota.pre.PCV,35F,197,357200,4,2,1,adjusted_type_specific_poisson,0.0158374119275726,0.00440919943413568,0.0349508338369155,0.213075270335225,0.153528489818432,0.28922843608303,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,3.1199701497318,0.868612288524729,6.88531426587234,0.847966923954691,0.202867790529554,2.04994238095218,1.1199701497318,0.152033076045309,No PCV -Bogota.pre.PCV,4,197,357200,4,2,5,adjusted_type_specific_poisson,0.00880692502641466,0.00339302808383035,0.0175301485670617,0.213075270335225,0.153528489818432,0.28922843608303,0.00249105790199758,0.00143369758150515,0.00400799422771078,1.73496423020369,0.668426532514579,3.45343926771115,6.25439583618021,2.66865383245399,11.3962508366447,0.265035769796311,1.25439583618021,PCV7 -Bogota.pre.PCV,5,197,357200,4,0,5,adjusted_type_specific_poisson,0.00239291147228062,0.000624934762847914,0.00583999708986559,0.213075270335225,0.153528489818432,0.28922843608303,0.00898185496955944,0.00375244500011871,0.0188069207217874,0.471403560039282,0.123112148281039,1.15047942670352,5.53084959184234,2.02327249455938,10.82911108406,0.471403560039282,0.530849591842337,PCV10 -Bogota.pre.PCV,6A,197,357200,4,23,16,adjusted_type_specific_poisson,0.118201955864758,0.0832441985980183,0.159398202982037,0.213075270335225,0.153528489818432,0.28922843608303,0.000470534749603847,0.000335293276070173,0.000638312814574088,23.2857853053573,16.3991071238096,31.4014459874613,16.5351093183069,11.2641925337078,22.9759203890532,0.285785305357347,0.535109318306873,PCV13 -Bogota.pre.PCV,6B,197,357200,4,12,26,adjusted_type_specific_poisson,0.0901044878166283,0.062182564987901,0.122856160112184,0.213075270335225,0.153528489818432,0.28922843608303,0.000770579380902745,0.000565085521465747,0.00101866271810419,17.7505840998758,12.2499653026165,24.2026635421002,20.631538633635,14.3408708944542,28.1207072420154,5.75058409987578,5.36846136636497,PCV7 -Bogota.pre.PCV,7C,197,357200,4,0,1,adjusted_type_specific_poisson,0.00634591681354683,0.000708320678197029,0.0184498079237747,0.213075270335225,0.153528489818432,0.28922843608303,0.000430538003690001,0.000121592824190092,0.000973102091763221,1.25014561226872,0.139539173604815,3.63461216098362,0.747637301699573,0.0726591510139654,2.32954529356477,1.25014561226872,0.252362698300427,No PCV -Bogota.pre.PCV,7F,197,357200,4,0,3,adjusted_type_specific_poisson,0.0012951758337783,0.000330249572061321,0.00302612049528048,0.213075270335225,0.153528489818432,0.28922843608303,0.00997721126084835,0.00681051079664878,0.01416409744657,0.255149639254326,0.0650591656960803,0.596145737570255,3.746889227775,1.04303082315881,8.24205043717506,0.255149639254326,0.746889227775005,PCV10 -Bogota.pre.PCV,8,197,357200,4,0,1,adjusted_type_specific_poisson,0.00227763292970677,0.000263190446592008,0.00679199495503164,0.213075270335225,0.153528489818432,0.28922843608303,0.00244545634969096,0.00123914949735586,0.00432306004960451,0.448693687152234,0.0518485179786257,1.33802300614123,1.5496360006774,0.190613792996939,4.31298107808961,0.448693687152234,0.5496360006774,PCV20 -Bogota.pre.PCV,9N,197,357200,4,5,2,adjusted_type_specific_poisson,0.0209665550941161,0.00836166010618227,0.0399059863202009,0.213075270335225,0.153528489818432,0.28922843608303,0.00065486417300752,0.000292518419108024,0.00122095961399422,4.13041135354088,1.64724704091791,7.86147930507958,3.87737939164186,1.50351307757077,7.50671642567282,0.86958864645912,1.87737939164186,PPV23 -Bogota.pre.PCV,9V,197,357200,4,0,8,adjusted_type_specific_poisson,0.00950250956592441,0.00400830287659094,0.0178325993720493,0.213075270335225,0.153528489818432,0.28922843608303,0.00259101673359874,0.00162148522659737,0.00391316735192488,1.87199438448711,0.789635666688414,3.51302207629371,7.11655558874063,3.22158082817005,12.4086246372335,1.87199438448711,0.883444411259368,PCV7 -Caracas.pre.PCV,1,1004,146125,1,0,2,adjusted_type_specific_poisson,0.0009979038017867,0.000190749092981242,0.00254269178010055,0.709439752718523,0.433190334815746,1.08190378642775,0.0206062908877376,0.0133467842050282,0.0309526551119594,1.00189541699385,0.191512089353167,2.55286254722095,2.00241074824905,0.401129549211904,4.94942100565269,1.00189541699385,0.00241074824905363,PCV10 -Caracas.pre.PCV,14,1004,146125,1,23,6,adjusted_type_specific_poisson,0.0201143375046401,0.0131573123014222,0.0285405210927644,0.709439752718523,0.433190334815746,1.08190378642775,0.00486577684119951,0.00359593248342883,0.00641271837258626,20.1947948546587,13.2099415506279,28.6546831771355,9.84425998590268,5.95811023451492,14.8765705360623,2.80520514534134,3.84425998590268,PCV7 -Caracas.pre.PCV,19A,1004,146125,1,32,3,adjusted_type_specific_poisson,0.0299746544177005,0.020968014446358,0.0408110136556886,0.709439752718523,0.433190334815746,1.08190378642775,0.00193665997116141,0.00151058619668583,0.00243196471893208,30.0945530353713,21.0518865041434,40.9742577103114,5.90687311843639,3.47596544764478,9.14577266340047,1.90544696462872,2.90687311843639,PCV13 -Caracas.pre.PCV,19F,1004,146125,1,3,2,adjusted_type_specific_poisson,0.00555131955726333,0.00204227640964493,0.0108064453973546,0.709439752718523,0.433190334815746,1.08190378642775,0.000752568056083617,0.000550123319373138,0.00100157805364369,5.57352483549238,2.05044551528351,10.849671178944,0.426309419932055,0.139386795839372,0.904613494727037,2.57352483549238,1.57369058006795,PCV7 -Caracas.pre.PCV,23F,1004,146125,1,25,1,adjusted_type_specific_poisson,0.024898016234255,0.016503068808319,0.0349512415594372,0.709439752718523,0.433190334815746,1.08190378642775,0.00077564137009531,0.000556479798610777,0.00105106918760042,24.9976082991921,16.5690810835523,35.0910465256749,1.96678528134481,1.05697080688894,3.27490893177742,0.00239170080794793,0.966785281344813,PCV7 -Caracas.pre.PCV,3,1004,146125,1,2,1,adjusted_type_specific_poisson,0.00325810864727418,0.000894973144975905,0.00715726269279848,0.709439752718523,0.433190334815746,1.08190378642775,0.00214630789735218,0.00150111695338643,0.00296037810122135,3.27114108186328,0.898553037555808,7.18589174356967,0.710196469626233,0.177599478648347,1.67739702644429,1.27114108186328,0.289803530373767,PCV13 -Caracas.pre.PCV,4,1004,146125,1,3,0,adjusted_type_specific_poisson,0.00319140162400421,0.000850964690712415,0.00705574299859257,0.709439752718523,0.433190334815746,1.08190378642775,0.00249105790199758,0.00143369758150515,0.00400799422771078,3.20416723050023,0.854368549475265,7.08396597058694,0.798269415030222,0.191137590782698,1.92839566465212,0.204167230500228,0.798269415030222,PCV7 -Caracas.pre.PCV,5,1004,146125,1,0,2,adjusted_type_specific_poisson,0.00163052917591856,0.000305345517508522,0.00417212180241535,0.709439752718523,0.433190334815746,1.08190378642775,0.00898185496955944,0.00375244500011871,0.0188069207217874,1.63705129262223,0.306566899578556,4.18881028962501,1.36869031293566,0.2543044005344,3.5950320172669,1.63705129262223,0.631309687064339,PCV10 -Caracas.pre.PCV,6A,1004,146125,1,20,3,adjusted_type_specific_poisson,0.0227322014521951,0.0145493795551949,0.0326333784911492,0.709439752718523,0.433190334815746,1.08190378642775,0.000470534749603847,0.000335293276070173,0.000638312814574088,22.8231302580039,14.6075770734157,32.7639120051138,1.09062413371738,0.567490811268277,1.85486622438349,2.82313025800392,1.90937586628262,PCV13 -Caracas.pre.PCV,6B,1004,146125,1,70,10,adjusted_type_specific_poisson,0.0744494886916739,0.059586092985942,0.0910273897929443,0.709439752718523,0.433190334815746,1.08190378642775,0.000770579380902745,0.000565085521465747,0.00101866271810419,74.7472866464405,59.8244373578858,91.3914993521161,5.84229739773026,3.55777766367886,8.82781127116868,4.74728664644054,4.15770260226974,PCV7 -Caracas.pre.PCV,7F,1004,146125,1,1,3,adjusted_type_specific_poisson,0.0024995908144523,0.000800126367281285,0.00529634313072247,0.709439752718523,0.433190334815746,1.08190378642775,0.00997721126084835,0.00681051079664878,0.01416409744657,2.50958917771011,0.80332687275041,5.31752850324536,2.47627261990987,0.77781521614429,5.23737020486074,1.50958917771011,0.523727380090129,PCV10 -Caracas.pre.PCV,9V,1004,146125,1,2,0,adjusted_type_specific_poisson,0.0023718069984305,0.000492407848877056,0.00581316080328543,0.709439752718523,0.433190334815746,1.08190378642775,0.00259101673359874,0.00162148522659737,0.00391316735192488,2.38129422642422,0.494377480272564,5.83641344649857,0.616947679671362,0.11838797802075,1.59471875981951,0.381294226424219,0.616947679671362,PCV7 -Czech.pre.PCV,1,425,478177,9,0,9,adjusted_type_specific_poisson,0.00158353746094423,0.000652461131294003,0.00309235125601783,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.0206062908877376,0.0133467842050282,0.0309526551119594,0.673003420901298,0.277295980799951,1.31424928380758,9.32729359211796,4.42773855055895,15.9953666856305,0.673003420901298,0.327293592117961,PCV10 -Czech.pre.PCV,10A,425,478177,9,6,4,adjusted_type_specific_poisson,0.0165684215512239,0.00811400959209263,0.0280828166871541,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000793695374669934,0.000513989148006867,0.00115253233769801,7.04157915927016,3.44845407663937,11.9351970920405,3.8962840103048,1.82236312730155,6.89526665883349,1.04157915927016,0.103715989695203,PCV20 -Czech.pre.PCV,11A,425,478177,9,8,1,adjusted_type_specific_poisson,0.0220684763367359,0.0107197880193761,0.0373297958040346,0.0707821692790444,0.0497841590798218,0.0973759059863025,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,9.37910244311277,4.55590990823482,15.8651632167147,0.56566926196961,0.2052047889476,1.17175017618199,1.37910244311277,0.43433073803039,PCV20 -Czech.pre.PCV,12F,425,478177,9,0,1,adjusted_type_specific_poisson,0.000784048732559159,8.72038984263272e-05,0.00238084082763525,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00763701563010158,0.00413184393687895,0.0128667210227945,0.333220711337643,0.0370616568311891,1.01185735174498,1.66510877104493,0.203887512694598,4.67571374511472,0.333220711337643,0.665108771044928,PCV20 -Czech.pre.PCV,14,425,478177,9,5,19,adjusted_type_specific_poisson,0.0134546425643981,0.00812426928210329,0.020415290426163,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00486577684119951,0.00359593248342883,0.00641271837258626,5.71822308986919,3.4528144448939,8.67649843111927,19.307009369853,12.3898514715073,27.7679110851226,0.718223089869192,0.30700936985302,PCV7 -Czech.pre.PCV,15B/C,425,478177,9,17,0,adjusted_type_specific_poisson,0.0330325445685807,0.0194564280382414,0.0500381861833507,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000410284575081173,0.000285934443755961,0.000563977573171364,14.0388314416468,8.26898191625258,21.266229127924,4.04599685006868,2.2129430697441,6.53936257300268,2.96116855835321,4.04599685006868,PCV20 -Czech.pre.PCV,17F,425,478177,9,0,1,adjusted_type_specific_poisson,0.00367572873215947,0.000454863240491285,0.0103715262756401,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000400957354522875,0.000201346292292629,0.000689191021815353,1.56218471116777,0.193316877208796,4.40789866714703,0.433615983265454,0.0499012498975184,1.27587936928361,1.56218471116777,0.566384016734546,PPV23 -Czech.pre.PCV,18C,425,478177,9,9,9,adjusted_type_specific_poisson,0.0134257533707122,0.00734370560689792,0.0217663537260057,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00341462550925104,0.0021814214974022,0.00511035484325696,5.7059451825527,3.12107488293162,9.25070033355241,13.3174301253325,7.9187209038197,20.2797641605082,3.2940548174473,4.31743012533253,PCV7 -Czech.pre.PCV,19A,425,478177,9,0,2,adjusted_type_specific_poisson,0.00299340862871236,0.000582611508738242,0.00735678070153722,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00193665997116141,0.00151058619668583,0.00243196471893208,1.27219866720275,0.247609891213753,3.12663179815332,1.72214756304023,0.340911538924717,4.22813352133053,1.27219866720275,0.277852436959768,PCV13 -Czech.pre.PCV,19F,425,478177,9,10,12,adjusted_type_specific_poisson,0.0351581197989244,0.0220075027101573,0.0516120458013709,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000752568056083617,0.000550123319373138,0.00100157805364369,14.9422009145429,9.35318865181685,21.9351194655826,7.88204851692838,4.72522553135248,11.9744756933442,4.94220091454288,4.11795148307162,PCV7 -Czech.pre.PCV,23A,425,478177,9,3,1,adjusted_type_specific_poisson,0.0103883773011652,0.00345368994700655,0.0211096906423328,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00017858253466746,0.000100358645533425,0.000284446850590249,4.41506035299523,1.46781822747779,8.97161852299143,0.55407528780658,0.160082815187892,1.25274482936956,1.41506035299523,0.44592471219342,No PCV -Czech.pre.PCV,23F,425,478177,9,30,13,adjusted_type_specific_poisson,0.0671149151123201,0.0483071494364265,0.0890686193195468,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00077564137009531,0.000556479798610777,0.00105106918760042,28.523838922736,20.5305385104813,37.8541632108074,15.4867374739297,10.5307280878522,21.5363995957637,1.47616107726396,2.48673747392973,PCV7 -Czech.pre.PCV,28F,425,478177,9,0,2,adjusted_type_specific_poisson,0.00467105888592268,0.000740496449771468,0.0123502129548927,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00103775197452743,6.89559651230105e-05,0.00439592363251434,1.98520002651714,0.314710991152874,5.24884050582938,1.00623698231764,0.0801971592065916,3.32213636941346,1.98520002651714,0.993763017682362,No PCV -Czech.pre.PCV,3,425,478177,9,6,5,adjusted_type_specific_poisson,0.0113405190654902,0.00564407489323556,0.0193283662403847,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00214630789735218,0.00150111695338643,0.00296037810122135,4.81972060283335,2.39873182962511,8.21455565216348,7.17384896911156,3.63195246600185,12.0393216051149,1.18027939716665,2.17384896911156,PCV13 -Czech.pre.PCV,33F,425,478177,9,0,1,adjusted_type_specific_poisson,0.00232214124266903,0.000274765993747428,0.00669214739098711,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00147980242560294,0.000904545029211608,0.00226255226693128,0.986910028134337,0.116775547342657,2.84416264116952,1.00344092552151,0.120679630363655,2.89859682234001,0.986910028134337,0.00344092552150532,PCV15 -Czech.pre.PCV,35F,425,478177,9,5,0,adjusted_type_specific_poisson,0.0125140934286875,0.00461255953699236,0.0243992962920011,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,5.31848970719219,1.96033780322175,10.3697009241005,0.678651655529027,0.196709874852303,1.55835203383905,0.31848970719219,0.678651655529027,No PCV -Czech.pre.PCV,37,425,478177,9,2,1,adjusted_type_specific_poisson,0.0085123302799211,0.00222743366583795,0.019083103794439,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000155201681937787,5.20169758717572e-06,0.000602123592537372,3.61774036896647,0.946659307981128,8.11031911263658,0.359642897505279,0.0105636457589775,1.4573380090953,1.61774036896647,0.640357102494721,No PCV -Czech.pre.PCV,38,425,478177,9,1,1,adjusted_type_specific_poisson,0.00406772564627636,0.000826432046321398,0.0100345467225391,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00107630112860654,0.000517329118040196,0.00192400799311281,1.72878339966745,0.351233619686594,4.26468235707913,1.25716317526503,0.248084304695407,3.16334032688506,0.728783399667454,0.257163175265034,No PCV -Czech.pre.PCV,4,425,478177,9,2,5,adjusted_type_specific_poisson,0.00700537809386967,0.00283632683466586,0.0133540282595588,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00249105790199758,0.00143369758150515,0.00400799422771078,2.97728568989461,1.20543890473299,5.67546201031247,5.0186051424861,2.10889033247711,9.23189553778231,0.977285689894611,0.0186051424861011,PCV7 -Czech.pre.PCV,40,425,478177,9,0,1,adjusted_type_specific_poisson,0.00233352534378153,5.60314220325456e-05,0.00852279810931375,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.0101875459431906,3.86224155460359e-05,0.0544998283429998,0.991748271107151,0.0238133543638319,3.62218919645834,1.00294515945426,0.0264441660171433,3.69149845132624,0.991748271107151,0.00294515945425644,No PCV -Czech.pre.PCV,5,425,478177,9,0,1,adjusted_type_specific_poisson,0.000722868104745053,7.32769896940574e-05,0.00229218131353008,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00898185496955944,0.00375244500011871,0.0188069207217874,0.307218944516647,0.0311427206199744,0.974177058250286,1.69089198963989,0.202481026648457,4.80907071453198,0.307218944516647,0.690891989639895,PCV10 -Czech.pre.PCV,6A,425,478177,9,24,8,adjusted_type_specific_poisson,0.0581767051475332,0.039888522033338,0.0796897078422404,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000470534749603847,0.000335293276070173,0.000638312814574088,24.7250996877016,16.9526218641687,33.8681258329522,8.16353006395037,5.17752900142744,11.9863388976726,0.725099687701604,0.163530063950367,PCV13 -Czech.pre.PCV,6B,425,478177,9,21,23,adjusted_type_specific_poisson,0.0677962519387166,0.048847716107403,0.0901597874897269,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.000770579380902745,0.000565085521465747,0.00101866271810419,28.8134070739546,20.7602793456463,38.3179096831339,15.5619788310107,10.7604300990318,21.4413616891896,7.81340707395455,7.43802116898927,PCV7 -Czech.pre.PCV,7F,425,478177,9,1,6,adjusted_type_specific_poisson,0.00241618485741106,0.000946281266142742,0.00470170042614674,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00997721126084835,0.00681051079664878,0.01416409744657,1.0268785643997,0.402169538110665,1.99822268111236,6.99538894188125,3.01018245689438,12.7079063426621,0.0268785643997007,0.995388941881245,PCV10 -Czech.pre.PCV,8,425,478177,9,1,1,adjusted_type_specific_poisson,0.0026947260922159,0.000527149273451624,0.00686035421681012,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00244545634969096,0.00123914949735586,0.00432306004960451,1.14525858919176,0.22403844121694,2.9156505421443,1.85883442736931,0.376104717878037,4.60151239251027,0.145258589191757,0.858834427369311,PCV20 -Czech.pre.PCV,9N,425,478177,9,1,2,adjusted_type_specific_poisson,0.00648381271715258,0.00175267713929998,0.0144777983410295,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00065486417300752,0.000292518419108024,0.00122095961399422,2.75562040478984,0.744887784202491,6.15306429493752,1.22554802240204,0.298273573268425,2.97339057404926,1.75562040478984,0.774451977597957,PPV23 -Czech.pre.PCV,9V,425,478177,9,1,9,adjusted_type_specific_poisson,0.00931947722094566,0.00431623666849046,0.016601278888314,0.0707821692790444,0.0497841590798218,0.0973759059863025,0.00259101673359874,0.00162148522659737,0.00391316735192488,3.9607778189019,1.83440058410844,7.05554352753347,7.01656198918585,3.38193578255907,12.0451929934305,2.9607778189019,1.98343801081415,PCV7 -France.post.PCV7,1,1212,838866,2,2,30,adjusted_type_specific_poisson,0.000844539386040749,0.000459036981330839,0.00138895966284539,1.16011992245611,0.865691607800223,1.53110807129231,0.0206062908877376,0.0133467842050282,0.0309526551119594,1.02358173588139,0.556352821372977,1.68341911136861,31.9668726458774,21.9880935000045,43.837179215796,0.976418264118613,1.96687264587738,PCV10 -France.post.PCV7,10A,1212,838866,2,0,7,adjusted_type_specific_poisson,0.00295150366825648,0.00122525831418641,0.0054960563200405,1.16011992245611,0.865691607800223,1.53110807129231,0.000793695374669934,0.000513989148006867,0.00115253233769801,3.57722244592686,1.48501307679393,6.66122025988909,4.4075523710516,1.86244905844864,8.10749923606978,3.57722244592686,2.5924476289484,PCV20 -France.post.PCV7,10B,1212,838866,2,0,1,adjusted_type_specific_poisson,0.000902345840237524,8.72034415058697e-05,0.0028165435383033,1.16011992245611,0.865691607800223,1.53110807129231,0.000696632980137251,9.61989918783685e-05,0.00234483425439832,1.09364315836788,0.105690571105114,3.4136507684236,0.91393214051049,0.0788822922530604,2.97762702944391,1.09364315836788,0.0860678594895102,No PCV -France.post.PCV7,11A,1212,838866,2,10,1,adjusted_type_specific_poisson,0.0087577680124937,0.00453930478403599,0.0144342379776718,1.16011992245611,0.865691607800223,1.53110807129231,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,10.6144148311424,5.50163739825162,17.4942964289382,1.42804337363284,0.571130632302708,2.80354510279577,0.614414831142359,0.428043373632844,PCV20 -France.post.PCV7,12B,1212,838866,2,1,1,adjusted_type_specific_poisson,0.00118191357005611,0.000130442065115633,0.00358124840461804,1.16011992245611,0.865691607800223,1.53110807129231,0.00125343072761337,7.75642593361291e-05,0.005419247182062,1.43247924690801,0.158095782920147,4.34047306639707,1.56035837470075,0.177539680416192,4.43725284729597,0.432479246908009,0.560358374700747,No PCV -France.post.PCV7,12F,1212,838866,2,0,9,adjusted_type_specific_poisson,0.000675695974039432,0.000256392907727148,0.0014002524571664,1.16011992245611,0.865691607800223,1.53110807129231,0.00763701563010158,0.00413184393687895,0.0128667210227945,0.818943520535792,0.310748204165304,1.69710597808567,9.15401085164087,4.39403023463472,15.6468862104637,0.818943520535792,0.154010851640866,PCV20 -France.post.PCV7,14,1212,838866,2,0,6,adjusted_type_specific_poisson,0.000672390408051238,0.000257921133319328,0.00129999465045894,1.16011992245611,0.865691607800223,1.53110807129231,0.00486577684119951,0.00359593248342883,0.00641271837258626,0.8149371745581,0.312600413583025,1.57559351635624,6.1785916633125,2.48931047352044,11.5787023367608,0.8149371745581,0.178591663312502,PCV7 -France.post.PCV7,15A,1212,838866,2,13,6,adjusted_type_specific_poisson,0.00971259504532852,0.00567781484177556,0.0149397684765351,1.16011992245611,0.865691607800223,1.53110807129231,0.000447893348168094,0.000276077603700969,0.000677854020290881,11.7716651949382,6.88151158823198,18.1069993935605,8.19673165777322,4.64012775813398,12.9197484336797,1.22833480506183,2.19673165777322,No PCV -France.post.PCV7,15B/C,1212,838866,2,23,17,adjusted_type_specific_poisson,0.0205405207017752,0.0145098298686443,0.027694411778594,1.16011992245611,0.865691607800223,1.53110807129231,0.000410284575081173,0.000285934443755961,0.000563977573171364,24.8951110905516,17.5859138007969,33.5656270756559,16.042011108428,10.9017971475636,22.3329997819692,1.89511109055158,0.957988891572029,PCV20 -France.post.PCV7,15F,1212,838866,2,1,0,adjusted_type_specific_poisson,0.00123985592710524,0.000139130659069975,0.00356329925362102,1.16011992245611,0.865691607800223,1.53110807129231,0.000241837303648991,2.36364376734738e-05,0.000792155722410316,1.50270538365155,0.16862635879281,4.31871869538868,0.487973871967231,0.0292812897155912,1.7717212415489,0.50270538365155,0.487973871967231,No PCV -France.post.PCV7,16F,1212,838866,2,0,1,adjusted_type_specific_poisson,0.000981768854025142,0.000114617265994385,0.00278176847342316,1.16011992245611,0.865691607800223,1.53110807129231,0.000442387133406364,0.000231326668676358,0.000740352472096137,1.18990385107847,0.138916126385194,3.37150338978887,0.804955190219275,0.094390121297173,2.32149998989762,1.18990385107847,0.195044809780725,No PCV -France.post.PCV7,17F,1212,838866,2,4,4,adjusted_type_specific_poisson,0.00459850430819889,0.00198965784365655,0.00839307760173454,1.16011992245611,0.865691607800223,1.53110807129231,0.000400957354522875,0.000201346292292629,0.000689191021815353,5.57338722153706,2.41146530651174,10.1724100533023,3.4211352905494,1.39916092368181,6.55554324929822,1.57338722153706,0.578864709450602,PPV23 -France.post.PCV7,18A,1212,838866,2,0,1,adjusted_type_specific_poisson,0.00119640201039202,0.000135698503262312,0.00349557587601956,1.16011992245611,0.865691607800223,1.53110807129231,0.000283343585215039,2.68111527639592e-05,0.000946066820544266,1.45003923659513,0.164466585953923,4.23663796173571,0.544209579039176,0.0317721223189056,1.99797790987673,1.45003923659513,0.455790420960824,No PCV -France.post.PCV7,18C,1212,838866,2,0,2,adjusted_type_specific_poisson,0.00039790427567513,7.56781000958208e-05,0.00100601763699593,1.16011992245611,0.865691607800223,1.53110807129231,0.00341462550925104,0.0021814214974022,0.00511035484325696,0.482259982118257,0.0917218573161348,1.21929337603907,2.51764090365203,0.516418550899328,6.04340343798664,0.482259982118257,0.517640903652032,PCV7 -France.post.PCV7,19A,1212,838866,2,28,128,adjusted_type_specific_poisson,0.0319652790518067,0.0251684085466153,0.0397513013272663,1.16011992245611,0.865691607800223,1.53110807129231,0.00193665997116141,0.00151058619668583,0.00243196471893208,38.7419182107897,30.5041111584977,48.1785772086468,117.957882881494,99.1925409277116,138.552716390913,10.7419182107897,10.0421171185063,PCV13 -France.post.PCV7,19F,1212,838866,2,8,10,adjusted_type_specific_poisson,0.00718092395224736,0.00419256627207128,0.0110790104466159,1.16011992245611,0.865691607800223,1.53110807129231,0.000752568056083617,0.000550123319373138,0.00100157805364369,8.7032798301238,5.08139032175039,13.4277606612984,10.2712037053431,6.0650155650617,15.5940270683015,0.703279830123799,0.271203705343051,PCV7 -France.post.PCV7,20,1212,838866,2,1,0,adjusted_type_specific_poisson,0.000733461216564761,7.22539717787228e-05,0.0022930989715251,1.16011992245611,0.865691607800223,1.53110807129231,0.000957797173992484,0.000238388518107766,0.00247568343665466,0.888954994476491,0.0875718137958121,2.77923595348843,1.12005992363398,0.118098810058183,3.34295701536979,0.111045005523509,1.12005992363398,PPV23 -France.post.PCV7,21,1212,838866,2,11,3,adjusted_type_specific_poisson,0.00909597872562439,0.00492136048635895,0.0145639799384037,1.16011992245611,0.865691607800223,1.53110807129231,0.000234606065585659,0.00010602199615295,0.000423079520489989,11.0243262154568,5.96468890946704,17.6515436853453,3.98138262861977,1.72842736821598,7.32209810427767,0.0243262154567638,0.981382628619768,No PCV -France.post.PCV7,22F,1212,838866,2,3,6,adjusted_type_specific_poisson,0.00302586345592852,0.00138487060566273,0.00540198439144501,1.16011992245611,0.865691607800223,1.53110807129231,0.00111291794656347,0.000747288532056908,0.00157611065350571,3.66734650858537,1.67846317406322,6.54720508243135,6.33799992029274,2.98501595115828,11.0527875604064,0.667346508585366,0.337999920292735,PCV15 -France.post.PCV7,23A,1212,838866,2,8,2,adjusted_type_specific_poisson,0.0070826661723819,0.0035289565093814,0.0119922826852913,1.16011992245611,0.865691607800223,1.53110807129231,0.00017858253466746,0.000100358645533425,0.000284446850590249,8.58419140092687,4.27709528937026,14.5346466145731,2.3977206614786,1.04910630131098,4.42507978456372,0.584191400926866,0.397720661478602,No PCV -France.post.PCV7,23B,1212,838866,2,10,3,adjusted_type_specific_poisson,0.00794492371701676,0.00429962445618006,0.0128090819339371,1.16011992245611,0.865691607800223,1.53110807129231,0.000290469676688038,0.000174295346379655,0.000444118199022155,9.62924754502431,5.21114484089023,15.5246073039318,4.36504657872022,2.20104349078067,7.50684295053214,0.370752454975692,1.36504657872022,No PCV -France.post.PCV7,23F,1212,838866,2,3,2,adjusted_type_specific_poisson,0.0022375343869413,0.000801941207496978,0.00445453073261864,1.16011992245611,0.865691607800223,1.53110807129231,0.00077564137009531,0.000556479798610777,0.00105106918760042,2.71189167697286,0.971952743486337,5.39889124793379,3.29401254863308,1.19427815195037,6.47539110136102,0.288108323027143,1.29401254863308,PCV7 -France.post.PCV7,24B,1212,838866,2,0,3,adjusted_type_specific_poisson,0.000628604635156895,4.0184190104201e-05,0.00228919114868721,1.16011992245611,0.865691607800223,1.53110807129231,0.00712047825808381,0.000499379415524034,0.0345762945937344,0.761868817810156,0.0487032384062916,2.7744996722089,3.21925648673351,0.766279942320435,7.33954018412219,0.761868817810156,0.219256486733513,No PCV -France.post.PCV7,24F,1212,838866,2,2,25,adjusted_type_specific_poisson,0.0042411934174918,0.00226347376039262,0.00707687425586109,1.16011992245611,0.865691607800223,1.53110807129231,0.00296592942741409,0.00168198604203905,0.00494246465975427,5.14032642200007,2.74333019759586,8.57717159810365,22.8113374411519,14.948069046369,32.3787416032708,3.14032642200007,2.18866255884813,No PCV -France.post.PCV7,25A,1212,838866,2,0,15,adjusted_type_specific_poisson,0.00342978446777076,0.00136895988844273,0.00661406222608617,1.16011992245611,0.865691607800223,1.53110807129231,0.00205858895387132,0.0008321684683761,0.00449630852733197,4.15689877493816,1.65917938479259,8.01624341801644,11.8583538748548,6.49325671304547,19.031567216634,4.15689877493816,3.14164612514523,No PCV -France.post.PCV7,28F,1212,838866,2,1,0,adjusted_type_specific_poisson,0.000827481865827446,6.54076575204765e-05,0.00274846234020369,1.16011992245611,0.865691607800223,1.53110807129231,0.00103775197452743,6.89559651230105e-05,0.00439592363251434,1.00290802138286,0.0792740809148175,3.33113635632688,0.99946238830184,0.0703989614972068,3.29835843749213,0.00290802138286472,0.99946238830184,No PCV -France.post.PCV7,29,1212,838866,2,3,0,adjusted_type_specific_poisson,0.002890467544904,0.000743659785804044,0.00651722716963187,1.16011992245611,0.865691607800223,1.53110807129231,0.000105704622446372,3.26554376138359e-06,0.000442922821034247,3.50324666442365,0.901315660394501,7.89887932959383,0.503352446595378,0.0155597270900602,2.0431086484691,0.503246664423648,0.503352446595378,No PCV -France.post.PCV7,3,1212,838866,2,1,18,adjusted_type_specific_poisson,0.00380038874624132,0.00214179915895199,0.00602657877627162,1.16011992245611,0.865691607800223,1.53110807129231,0.00214630789735218,0.00150111695338643,0.00296037810122135,4.60607116044448,2.59586058064981,7.30421347684121,15.3519872069485,9.35272190132221,22.8412635734474,3.60607116044448,2.6480127930515,PCV13 -France.post.PCV7,31,1212,838866,2,0,2,adjusted_type_specific_poisson,0.00139654757531463,0.000270269076082316,0.00351866726525111,1.16011992245611,0.865691607800223,1.53110807129231,0.000529235275657269,0.000187950733188048,0.00110145716265855,1.69261566128133,0.327566120211767,4.26462472548434,1.30860661415499,0.240554783777415,3.41379896960385,1.69261566128133,0.691393385845007,No PCV -France.post.PCV7,33F,1212,838866,2,3,5,adjusted_type_specific_poisson,0.00227319670865295,0.000952316932198427,0.00423822571042466,1.16011992245611,0.865691607800223,1.53110807129231,0.00147980242560294,0.000904545029211608,0.00226255226693128,2.75511441088737,1.15420812182449,5.13672956103468,6.23970253218352,2.80996651378473,11.063505061077,0.244885589112626,1.23970253218352,PCV15 -France.post.PCV7,34,1212,838866,2,1,0,adjusted_type_specific_poisson,0.00139232208704855,0.000165778474816976,0.00389448321905594,1.16011992245611,0.865691607800223,1.53110807129231,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,1.68749436950284,0.200923511478176,4.72011366149579,0.30211842741373,0.022312539999555,1.06787212985092,0.687494369502839,0.30211842741373,No PCV -France.post.PCV7,35B,1212,838866,2,8,1,adjusted_type_specific_poisson,0.00672577071562944,0.00322233219575396,0.0116110386023968,1.16011992245611,0.865691607800223,1.53110807129231,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,8.15163410734288,3.9054666212538,14.0725787861049,1.83440832614185,0.681870731627433,3.71252545686647,0.151634107342884,0.834408326141845,No PCV -France.post.PCV7,35F,1212,838866,2,7,3,adjusted_type_specific_poisson,0.00704471166722163,0.0034553752608608,0.0119602748499543,1.16011992245611,0.865691607800223,1.53110807129231,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,8.53819054067261,4.18791481616329,14.4958531181447,2.41085825396442,0.947359415004928,4.68225566158594,1.53819054067261,0.58914174603558,No PCV -France.post.PCV7,4,1212,838866,2,2,0,adjusted_type_specific_poisson,0.000521378346808313,0.00010056093122006,0.00135231845332381,1.16011992245611,0.865691607800223,1.53110807129231,0.00249105790199758,0.00143369758150515,0.00400799422771078,0.631910556331676,0.121879848638713,1.63900996542846,2.36889218349997,0.482764321455732,5.70900687639458,1.36808944366832,2.36889218349997,PCV7 -France.post.PCV7,45,1212,838866,2,1,0,adjusted_type_specific_poisson,0.00150803167813394,0.000176915542441651,0.00430195918925763,1.16011992245611,0.865691607800223,1.53110807129231,9.68276084459584e-05,1.14155848047784e-06,0.00073570031655298,1.82773439389833,0.214421637439282,5.21397453738025,0.174929556251032,0.00144082109473086,1.23375751253486,0.827734393898333,0.174929556251032,No PCV -France.post.PCV7,46,1212,838866,2,0,1,adjusted_type_specific_poisson,2.78614564174549e-05,6.46015329337447e-07,0.000155636868820806,1.16011992245611,0.865691607800223,1.53110807129231,0.136429955213569,0.00745390261250882,0.684777891126085,0.0337680851779553,0.000782970579156985,0.188631885010817,1.9867076331183,0.243631231650777,5.53131257981453,0.0337680851779553,0.986707633118299,No PCV -France.post.PCV7,5,1212,838866,2,0,4,adjusted_type_specific_poisson,0.000312828448346893,7.48039673816324e-05,0.000800963820525634,1.16011992245611,0.865691607800223,1.53110807129231,0.00898185496955944,0.00375244500011871,0.0188069207217874,0.379148079396434,0.0906624084665385,0.970768150477069,4.6278479560898,1.50168166022441,9.51379176224854,0.379148079396434,0.6278479560898,PCV10 -France.post.PCV7,6A,1212,838866,2,10,3,adjusted_type_specific_poisson,0.00664389555177184,0.00356824347839363,0.0107668907063099,1.16011992245611,0.865691607800223,1.53110807129231,0.000470534749603847,0.000335293276070173,0.000638312814574088,8.05240140874747,4.32471109581308,13.0494715360476,5.95085925283783,3.15717001924398,9.72936992094572,1.94759859125253,2.95085925283783,PCV13 -France.post.PCV7,6B,1212,838866,2,3,4,adjusted_type_specific_poisson,0.00299001276431614,0.00126626473264948,0.00547251230171845,1.16011992245611,0.865691607800223,1.53110807129231,0.000770579380902745,0.000565085521465747,0.00101866271810419,3.62389547035117,1.53471285597117,6.63268490968276,4.38563313152649,1.86472002233645,8.03526720818933,0.623895470351166,0.38563313152649,PCV7 -France.post.PCV7,6C,1212,838866,2,13,4,adjusted_type_specific_poisson,0.0127882174284382,0.00745867182167583,0.0197176728216212,1.16011992245611,0.865691607800223,1.53110807129231,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,15.4993195232671,9.03991024787111,23.897819459805,2.46859939782837,0.991416046586293,4.7528234758594,2.49931952326713,1.53140060217163,No PCV -France.post.PCV7,7C,1212,838866,2,0,1,adjusted_type_specific_poisson,0.00101612542393928,0.000117934880260517,0.00293143936416753,1.16011992245611,0.865691607800223,1.53110807129231,0.000430538003690001,0.000121592824190092,0.000973102091763221,1.2315440138144,0.142937074875747,3.55290450937105,0.761376380314587,0.0808234871932894,2.34863974156085,1.2315440138144,0.238623619685413,No PCV -France.post.PCV7,7F,1212,838866,2,2,53,adjusted_type_specific_poisson,0.00283089189444686,0.00175909131510566,0.00426356835856685,1.16011992245611,0.865691607800223,1.53110807129231,0.00997721126084835,0.00681051079664878,0.01416409744657,3.43104097606959,2.13201867390806,5.16744485058302,52.5932921621397,39.6770171518207,67.5311004920666,1.43104097606959,0.406707837860282,PCV10 -France.post.PCV7,8,1212,838866,2,1,1,adjusted_type_specific_poisson,0.000542051553805127,0.000100355801306084,0.00141344498590269,1.16011992245611,0.865691607800223,1.53110807129231,0.00244545634969096,0.00123914949735586,0.00432306004960451,0.656966483211814,0.121631231182973,1.71309532291406,2.36021979149481,0.495033307712675,5.72912438681542,0.343033516788186,1.36021979149481,PCV20 -France.post.PCV7,9A,1212,838866,2,0,1,adjusted_type_specific_poisson,0.0010366794681232,8.1163878462631e-05,0.00337096011462372,1.16011992245611,0.865691607800223,1.53110807129231,0.000693492945095352,1.08310516244248e-05,0.0036545591314838,1.25645551536532,0.0983706206967088,4.08560365892395,0.734052735636849,0.0182761399304348,2.89124301169943,1.25645551536532,0.265947264363151,No PCV -France.post.PCV7,9L,1212,838866,2,0,1,adjusted_type_specific_poisson,0.000413264623015118,1.3176138966539e-05,0.00184824411232754,1.16011992245611,0.865691607800223,1.53110807129231,0.00651481161652821,0.000202150097442497,0.0350412259425872,0.500876723094323,0.0159694804274452,2.24007186414098,1.4972931938657,0.140215436430476,4.47906359483556,0.500876723094323,0.497293193865695,No PCV -France.post.PCV7,9N,1212,838866,2,1,1,adjusted_type_specific_poisson,0.00125102123906911,0.000243167927523017,0.00315889331759893,1.16011992245611,0.865691607800223,1.53110807129231,0.00065486417300752,0.000292518419108024,0.00122095961399422,1.51623774175176,0.294719528157896,3.8285787009299,1.48149761019593,0.282710920047296,3.75731970514105,0.516237741751763,0.481497610195926,PPV23 -France.post.PCV7,9V,1212,838866,2,0,2,adjusted_type_specific_poisson,0.000500107987682355,9.83960271940426e-05,0.00126701110258831,1.16011992245611,0.865691607800223,1.53110807129231,0.00259101673359874,0.00162148522659737,0.00391316735192488,0.606130881071014,0.11925598495918,1.53561745633703,2.3986281917778,0.493176976656679,5.78278818569766,0.606130881071014,0.398628191777804,PCV7 -Goroka.pre.PCV,1,2844,96207,6,1,1,adjusted_type_specific_poisson,0.000799618032015412,0.000165248368911778,0.00194756964258305,0.0786913745437151,0.040686874985607,0.13259606325277,0.0206062908877376,0.0133467842050282,0.0309526551119594,2.27411368305183,0.469966361185095,5.5388880635062,0.721419148835011,0.132837598222617,1.92557459164309,1.27411368305183,0.278580851164989,PCV10 -Goroka.pre.PCV,13,2844,96207,6,45,1,adjusted_type_specific_poisson,0.0162982078677526,0.0119665637900458,0.0212383417172026,0.0786913745437151,0.040686874985607,0.13259606325277,0.000869816776002311,0.000245481001501479,0.00212058387716859,46.3521031758884,34.0329074188902,60.401843843724,0.622833332361565,0.15496862540687,1.60082211169543,1.35210317588844,0.377166667638435,No PCV -Goroka.pre.PCV,14,2844,96207,6,118,7,adjusted_type_specific_poisson,0.0411587569132288,0.0342594520704323,0.0485516917234838,0.0786913745437151,0.040686874985607,0.13259606325277,0.00486577684119951,0.00359593248342883,0.00641271837258626,117.055504661223,97.4338816883093,138.081011261588,8.89230860147051,4.83213288242001,14.273382920669,0.944495338777429,1.89230860147051,PCV7 -Goroka.pre.PCV,2,2844,96207,6,2,1,adjusted_type_specific_poisson,0.00125564129015952,0.000321720898339766,0.00281962383026866,0.0786913745437151,0.040686874985607,0.13259606325277,0.00998959870125364,0.000295715381084731,0.0530573529119405,3.57104382921367,0.914974234878295,8.01901017328408,0.428932563400612,0.0125485294396049,2.06611433172026,1.57104382921367,0.571067436599388,PPV23 -Goroka.pre.PCV,20,2844,96207,6,12,0,adjusted_type_specific_poisson,0.00448928931685627,0.00238777556651347,0.00721411882938142,0.0786913745437151,0.040686874985607,0.13259606325277,0.000957797173992484,0.000238388518107766,0.00247568343665466,12.7675388171392,6.79083371116431,20.5169539507608,0.191107243230541,0.0367412262983331,0.556031398759657,0.76753881713922,0.191107243230541,PPV23 -Goroka.pre.PCV,21,2844,96207,6,45,0,adjusted_type_specific_poisson,0.016088053201641,0.0118625669711118,0.0208858141401364,0.0786913745437151,0.040686874985607,0.13259606325277,0.000234606065585659,0.00010602199615295,0.000423079520489989,45.7544233054669,33.737140465842,59.399255414548,0.16968189168043,0.059191852194871,0.37061261878315,0.754423305466865,0.16968189168043,No PCV -Goroka.pre.PCV,29,2844,96207,6,22,0,adjusted_type_specific_poisson,0.00807803470396337,0.00512145926436212,0.0116865998823541,0.0786913745437151,0.040686874985607,0.13259606325277,0.000105704622446372,3.26554376138359e-06,0.000442922821034247,22.9739306980718,14.5654301478459,33.2366900654151,0.0380083200996836,0.00107389400929196,0.166334889301226,0.973930698071833,0.0380083200996836,No PCV -Goroka.pre.PCV,3,2844,96207,6,23,0,adjusted_type_specific_poisson,0.00816407833519992,0.00519597513629807,0.0117419224451413,0.0786913745437151,0.040686874985607,0.13259606325277,0.00214630789735218,0.00150111695338643,0.00296037810122135,23.2186387853086,14.7773532876317,33.3940274339819,0.784728398912163,0.345135331663798,1.46929850679353,0.218638785308578,0.784728398912163,PCV13 -Goroka.pre.PCV,31,2844,96207,6,14,1,adjusted_type_specific_poisson,0.00557092415466008,0.00318060085576436,0.00862216591124754,0.0786913745437151,0.040686874985607,0.13259606325277,0.000529235275657269,0.000187950733188048,0.00110145716265855,15.8437082958533,9.04562883379385,24.521439851588,0.132561964417032,0.0344013709814334,0.334791077941642,1.84370829585326,0.867438035582968,No PCV -Goroka.pre.PCV,34,2844,96207,6,44,1,adjusted_type_specific_poisson,0.016144422940284,0.011863171134185,0.0211249222106254,0.0786913745437151,0.040686874985607,0.13259606325277,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,45.9147388421677,33.7388587056221,60.0792787670187,0.0856809204653993,0.0145350347166506,0.24232536785812,1.91473884216773,0.914319079534601,No PCV -Goroka.pre.PCV,36,2844,96207,6,1,0,adjusted_type_specific_poisson,0.000699438714962011,8.67215810509864e-05,0.00196126851233615,0.0786913745437151,0.040686874985607,0.13259606325277,0.000211384916000071,1.20317230766708e-06,0.00166520932006513,1.98920370535196,0.246636176509005,5.577847649084,0.0063028035718979,1.45619297129228e-05,0.0502782870709881,0.98920370535196,0.0063028035718979,No PCV -Goroka.pre.PCV,38,2844,96207,6,21,0,adjusted_type_specific_poisson,0.00761628808104572,0.00479607273754821,0.0110369528051081,0.0786913745437151,0.040686874985607,0.13259606325277,0.00107630112860654,0.000517329118040196,0.00192400799311281,21.660723302494,13.6400308655871,31.3890937777275,0.367026996421831,0.128237987137001,0.803385343435628,0.660723302494027,0.367026996421831,No PCV -Goroka.pre.PCV,39,2844,96207,6,4,0,adjusted_type_specific_poisson,0.00171290609696545,0.000550354046098098,0.00354821164506393,0.0786913745437151,0.040686874985607,0.13259606325277,0.00186570134034449,1.26690467080328e-06,0.0163413392281048,4.87150493976973,1.56520690710299,10.0911139185618,0.110514212758107,6.97633055728223e-05,0.989411742822395,0.87150493976973,0.110514212758107,No PCV -Goroka.pre.PCV,4,2844,96207,6,27,0,adjusted_type_specific_poisson,0.00947681277697247,0.0063139622053719,0.0132839353686792,0.0786913745437151,0.040686874985607,0.13259606325277,0.00249105790199758,0.00143369758150515,0.00400799422771078,26.9520555377097,17.9569085120777,37.7795121885238,1.04825609196829,0.438085391153223,2.02281734606609,0.047944462290296,1.04825609196829,PCV7 -Goroka.pre.PCV,42,2844,96207,6,14,0,adjusted_type_specific_poisson,0.00525810558068554,0.00292716199464615,0.00826206691598459,0.0786913745437151,0.040686874985607,0.13259606325277,0.000106976485278402,1.13850123454097e-06,0.000791514809070834,14.9540522714697,8.32484871277365,23.4973183090602,0.0247198956848206,0.000210917306414082,0.18513254800116,0.954052271469681,0.0247198956848206,No PCV -Goroka.pre.PCV,43,2844,96207,6,1,0,adjusted_type_specific_poisson,0.000668896104060389,7.48947134041578e-05,0.00189716154572195,0.0786913745437151,0.040686874985607,0.13259606325277,0.00667665426115096,1.2842177651341e-06,0.0554209457186083,1.90234051994775,0.213000564921425,5.39552743603323,0.101189904485139,1.85648552750167e-05,0.937164614347257,0.902340519947746,0.101189904485139,No PCV -Goroka.pre.PCV,45,2844,96207,6,7,0,adjusted_type_specific_poisson,0.00280992854654815,0.00120858534711159,0.00506752783014051,0.0786913745437151,0.040686874985607,0.13259606325277,9.68276084459584e-05,1.14155848047784e-06,0.00073570031655298,7.99143678638294,3.43721672718535,14.4120491489196,0.0120162832223013,0.000100386183974297,0.0932502224652347,0.991436786382938,0.0120162832223013,No PCV -Goroka.pre.PCV,46,2844,96207,6,0,3,adjusted_type_specific_poisson,0.00069347046601858,8.28151679797991e-05,0.00192956564355143,0.0786913745437151,0.040686874985607,0.13259606325277,0.136429955213569,0.00745390261250882,0.684777891126085,1.97223000535684,0.235526337734549,5.48768469026027,2.02322342227569,0.263555180266832,5.54301406442952,1.97223000535684,0.976776577724313,No PCV -Goroka.pre.PCV,47,2844,96207,6,1,0,adjusted_type_specific_poisson,0.00066823819933664,7.3703146375014e-05,0.00192467778956516,0.0786913745437151,0.040686874985607,0.13259606325277,0.00619035016021828,1.29650232153249e-06,0.0530799497370932,1.9004694389134,0.20961174829054,5.47378363352331,0.0961063660688174,1.91074059420202e-05,0.883322307603576,0.900469438913405,0.0961063660688174,No PCV -Goroka.pre.PCV,5,2844,96207,6,5,2,adjusted_type_specific_poisson,0.0024733863816846,0.00105233219777671,0.00450620702762683,0.0786913745437151,0.040686874985607,0.13259606325277,0.00898185496955944,0.00375244500011871,0.0188069207217874,7.03431086951099,2.99283277047696,12.8156527865707,0.959777676079165,0.269130698900626,2.31492005456279,2.03431086951099,1.04022232392083,PCV10 -Goroka.pre.PCV,8,2844,96207,6,9,0,adjusted_type_specific_poisson,0.00338531419117747,0.00159512840241873,0.00585149288731133,0.0786913745437151,0.040686874985607,0.13259606325277,0.00244545634969096,0.00123914949735586,0.00432306004960451,9.62783355970872,4.53654517647888,16.6416457715134,0.369378250126096,0.11412298542948,0.861272799477133,0.627833559708725,0.369378250126096,PCV20 -Massachusetts.post.PCV7,1,2969,820000,3,0,1,adjusted_type_specific_poisson,9.80570932841296e-05,1.10650238137004e-05,0.000286834014813002,0.363495562185596,0.276041416147802,0.470834966111799,0.0206062908877376,0.0133467842050282,0.0309526551119594,0.291131509960581,0.0328520557028765,0.851610189979804,1.71637206581354,0.204811764231579,4.79931043694695,0.291131509960581,0.716372065813537,PCV10 -Massachusetts.post.PCV7,10A,2969,820000,3,27,4,adjusted_type_specific_poisson,0.00872556173435204,0.00588700811653912,0.0121136505783355,0.363495562185596,0.276041416147802,0.470834966111799,0.000793695374669934,0.000513989148006867,0.00115253233769801,25.9061927892912,17.4785270980046,35.965428567078,6.07843874754713,3.6424921972332,9.2539435106583,1.0938072107088,2.07843874754713,PCV20 -Massachusetts.post.PCV7,11A,2969,820000,3,63,3,adjusted_type_specific_poisson,0.0219997471306874,0.0170414267118615,0.0275169850021393,0.363495562185596,0.276041416147802,0.470834966111799,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,65.317249231011,50.5959959075169,81.6979284713517,1.6634408640627,0.791499056689015,2.91447673700609,2.31724923101102,1.3365591359373,PCV20 -Massachusetts.post.PCV7,12B,2969,820000,3,0,1,adjusted_type_specific_poisson,0.000527609851054927,5.58415926728917e-05,0.00153876380650849,0.363495562185596,0.276041416147802,0.470834966111799,0.00125343072761337,7.75642593361291e-05,0.005419247182062,1.56647364778208,0.165793688645816,4.56858974152371,0.429704529719597,0.0180722930391721,1.77098747681496,1.56647364778208,0.570295470280403,No PCV -Massachusetts.post.PCV7,13,2969,820000,3,1,0,adjusted_type_specific_poisson,0.000545048968095855,6.55129456797083e-05,0.00155884026391297,0.363495562185596,0.276041416147802,0.470834966111799,0.000869816776002311,0.000245481001501479,0.00212058387716859,1.61825038627659,0.194507935723054,4.62819674355762,0.394482964661657,0.0361394638795588,1.30986285772394,0.618250386276592,0.394482964661657,No PCV -Massachusetts.post.PCV7,14,2969,820000,3,3,1,adjusted_type_specific_poisson,0.000693685832268613,0.000217829960514267,0.00144804961903912,0.363495562185596,0.276041416147802,0.470834966111799,0.00486577684119951,0.00359593248342883,0.00641271837258626,2.05955323600551,0.64673715276686,4.29925931892714,2.95218988208064,0.939972993125861,6.10450062071104,0.940446763994486,1.95218988208064,PCV7 -Massachusetts.post.PCV7,15A,2969,820000,3,36,3,adjusted_type_specific_poisson,0.0119114572229894,0.00850381506041799,0.0158832100871278,0.363495562185596,0.276041416147802,0.470834966111799,0.000447893348168094,0.000276077603700969,0.000677854020290881,35.3651164950555,25.247826914381,47.1572507486823,4.69530176288728,2.73642724080279,7.40138368444944,0.634883504944526,1.69530176288728,No PCV -Massachusetts.post.PCV7,15B/C,2969,820000,3,74,8,adjusted_type_specific_poisson,0.0249159377869609,0.0197885973995612,0.0306289097987461,0.363495562185596,0.276041416147802,0.470834966111799,0.000410284575081173,0.000285934443755961,0.000563977573171364,73.9754192894869,58.7523456792972,90.9372331924771,9.01358050414968,6.17936260789443,12.5526683572736,0.0245807105131064,1.01358050414968,PCV20 -Massachusetts.post.PCV7,15F,2969,820000,3,4,0,adjusted_type_specific_poisson,0.00157413724905452,0.000510550348987302,0.0032467144380413,0.363495562185596,0.276041416147802,0.470834966111799,0.000241837303648991,2.36364376734738e-05,0.000792155722410316,4.67361349244287,1.5158239861433,9.63949516654461,0.320498070457278,0.0257698495499747,1.13455272365311,0.673613492442866,0.320498070457278,No PCV -Massachusetts.post.PCV7,16F,2969,820000,3,13,0,adjusted_type_specific_poisson,0.00416560652961984,0.00226892192762176,0.00664636293143148,0.363495562185596,0.276041416147802,0.470834966111799,0.000442387133406364,0.000231326668676358,0.000740352472096137,12.3676857864413,6.73642920310902,19.7330515434201,1.61458794545334,0.700294701890929,3.07702916701295,0.632314213558706,1.61458794545334,No PCV -Massachusetts.post.PCV7,17F,2969,820000,3,8,1,adjusted_type_specific_poisson,0.00301121205779955,0.00142194611842252,0.00516582496385056,0.363495562185596,0.276041416147802,0.470834966111799,0.000400957354522875,0.000201346292292629,0.000689191021815353,8.94028859960686,4.22175802559647,15.3373343176723,1.05972827970927,0.399433430881269,2.18029032633692,0.940288599606863,0.0597282797092664,PPV23 -Massachusetts.post.PCV7,18B,2969,820000,3,0,2,adjusted_type_specific_poisson,0.000703317450456694,0.000131350803517389,0.00178874663096493,0.363495562185596,0.276041416147802,0.470834966111799,0.00173622469177418,0.00030591934704866,0.00552384967796135,2.08814951040592,0.389980535643129,5.31078874733488,0.908438658111017,0.116891989846349,2.79284792890513,2.08814951040592,1.09156134188898,No PCV -Massachusetts.post.PCV7,18C,2969,820000,3,2,4,adjusted_type_specific_poisson,0.00118078736475059,0.000464794495948049,0.00225800125400891,0.363495562185596,0.276041416147802,0.470834966111799,0.00341462550925104,0.0021814214974022,0.00511035484325696,3.5057576859445,1.37997485846976,6.70400572315246,3.48889111059493,1.37008407576722,6.67048259932054,1.5057576859445,0.51110888940507,PCV7 -Massachusetts.post.PCV7,18F,2969,820000,3,1,0,adjusted_type_specific_poisson,0.000524118940089075,5.60283692922951e-05,0.00155253060731057,0.363495562185596,0.276041416147802,0.470834966111799,0.00126829626653312,7.78271438048081e-05,0.00564867594935307,1.55610913312446,0.166348228428824,4.60946337310509,0.440486462268766,0.0182859450540192,1.81310671129857,0.556109133124464,0.440486462268766,No PCV -Massachusetts.post.PCV7,19A,2969,820000,3,113,80,adjusted_type_specific_poisson,0.0414184477708778,0.0352441880409415,0.0482610572509991,0.363495562185596,0.276041416147802,0.470834966111799,0.00193665997116141,0.00151058619668583,0.00243196471893208,122.971371431736,104.639994293555,143.287078978216,70.6585184307919,57.7078859749468,85.0411444007695,9.97137143173633,9.34148156920807,PCV13 -Massachusetts.post.PCV7,19F,2969,820000,3,31,2,adjusted_type_specific_poisson,0.00936873630673213,0.00642428854139297,0.0128250452182052,0.363495562185596,0.276041416147802,0.470834966111799,0.000752568056083617,0.000550123319373138,0.00100157805364369,27.8157780946877,19.0737126793957,38.0775592528513,6.21307607309646,3.96813605832738,9.07536927332231,3.18422190531231,4.21307607309646,PCV7 -Massachusetts.post.PCV7,20,2969,820000,3,0,2,adjusted_type_specific_poisson,0.000795960285368717,0.000163418990494805,0.00195239862541874,0.363495562185596,0.276041416147802,0.470834966111799,0.000957797173992484,0.000238388518107766,0.00247568343665466,2.36320608725972,0.485190982779076,5.79667151886824,0.626108326775764,0.088599910203521,1.86040394749384,2.36320608725972,1.37389167322424,PPV23 -Massachusetts.post.PCV7,21,2969,820000,3,7,1,adjusted_type_specific_poisson,0.00282928384000489,0.00130997280788817,0.00491531178342052,0.363495562185596,0.276041416147802,0.470834966111799,0.000234606065585659,0.00010602199615295,0.000423079520489989,8.40014372097452,3.88930926661999,14.5935606849755,0.583299381095453,0.195532566484352,1.25642510787351,1.40014372097452,0.416700618904547,No PCV -Massachusetts.post.PCV7,22F,2969,820000,3,26,14,adjusted_type_specific_poisson,0.0103769245745495,0.0074167869767238,0.013940124547541,0.363495562185596,0.276041416147802,0.470834966111799,0.00111291794656347,0.000747288532056908,0.00157611065350571,30.8090890618375,22.020440533893,41.3882297816492,10.1406565100682,6.48008357319949,14.8705332169114,4.80908906183754,3.85934348993185,PCV15 -Massachusetts.post.PCV7,23A,2969,820000,3,62,1,adjusted_type_specific_poisson,0.0204844817904926,0.0157699897608946,0.0258062159732653,0.363495562185596,0.276041416147802,0.470834966111799,0.00017858253466746,0.000100358645533425,0.000284446850590249,60.8184264359725,46.8210996000959,76.6186552246246,3.22373189821447,1.76940566467938,5.22043943535626,1.18157356402747,2.22373189821447,No PCV -Massachusetts.post.PCV7,23B,2969,820000,3,43,6,adjusted_type_specific_poisson,0.0154981706446433,0.0114770812969834,0.0200746367095724,0.363495562185596,0.276041416147802,0.470834966111799,0.000290469676688038,0.000174295346379655,0.000444118199022155,46.014068643946,34.0754543707438,59.6015963907205,3.96459224547211,2.29743088480287,6.20179623231127,3.01406864394602,2.03540775452789,No PCV -Massachusetts.post.PCV7,23F,2969,820000,3,5,2,adjusted_type_specific_poisson,0.00219180111902745,0.000949401068544825,0.00396151564623998,0.363495562185596,0.276041416147802,0.470834966111799,0.00077564137009531,0.000556479798610777,0.00105106918760042,6.50745752239248,2.81877177250958,11.7617399536865,1.49797330879343,0.612434855251207,2.81867831136882,1.50745752239248,0.502026691206568,PCV7 -Massachusetts.post.PCV7,25A,2969,820000,3,3,0,adjusted_type_specific_poisson,0.000857747595864442,0.000220728295385496,0.00194172904463844,0.363495562185596,0.276041416147802,0.470834966111799,0.00205858895387132,0.0008321684683761,0.00449630852733197,2.54665261212153,0.655342308999538,5.76499353353152,1.4551830243266,0.348239957425807,3.55976673456328,0.453347387878472,1.4551830243266,No PCV -Massachusetts.post.PCV7,3,2969,820000,3,11,8,adjusted_type_specific_poisson,0.00412431463313881,0.00246487385885672,0.00620959162037401,0.363495562185596,0.276041416147802,0.470834966111799,0.00214630789735218,0.00150111695338643,0.00296037810122135,12.2450901457891,7.31821048694559,18.4362775208904,7.75402256282527,4.54790526797033,11.9879234591441,1.24509014578914,0.245977437174729,PCV13 -Massachusetts.post.PCV7,31,2969,820000,3,7,0,adjusted_type_specific_poisson,0.00233114178357403,0.0010034048411692,0.00424809709590986,0.363495562185596,0.276041416147802,0.470834966111799,0.000529235275657269,0.000187950733188048,0.00110145716265855,6.92115995543129,2.97910897343135,12.6126002777564,1.06502313576456,0.303699601455521,2.45654230859885,0.0788400445687136,1.06502313576456,No PCV -Massachusetts.post.PCV7,33A,2969,820000,3,1,0,adjusted_type_specific_poisson,0.000653040800578559,7.83149013539482e-05,0.00181716372612308,0.363495562185596,0.276041416147802,0.470834966111799,0.000126887088118296,1.17148310590837e-06,0.000937616322945586,1.93887813691774,0.232516942119872,5.39515910285943,0.0624990865599309,0.000273430885052353,0.473197283515277,0.938878136917743,0.0624990865599309,No PCV -Massachusetts.post.PCV7,33F,2969,820000,3,6,11,adjusted_type_specific_poisson,0.00422043923226515,0.00245900049088154,0.0064951021432824,0.363495562185596,0.276041416147802,0.470834966111799,0.00147980242560294,0.000904545029211608,0.00226255226693128,12.5304840805952,7.30077245742728,19.2839582634054,5.44459154046022,2.89386411093388,8.95362265491473,6.53048408059523,5.55540845953978,PCV15 -Massachusetts.post.PCV7,34,2969,820000,3,12,0,adjusted_type_specific_poisson,0.00422294484800762,0.00222179914558193,0.00679737580518706,0.363495562185596,0.276041416147802,0.470834966111799,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,12.5379232537346,6.59652166323274,20.1814087656004,0.436578320507729,0.0766774011301958,1.16673453527259,0.537923253734627,0.436578320507729,No PCV -Massachusetts.post.PCV7,35B,2969,820000,3,65,0,adjusted_type_specific_poisson,0.0213042120145224,0.0165887354466178,0.0265965772747342,0.363495562185596,0.276041416147802,0.470834966111799,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,63.252205471117,49.2519555410082,78.965237928686,2.70838077847501,1.25603069459066,4.83073436348965,1.74779452888297,2.70838077847501,No PCV -Massachusetts.post.PCV7,35F,2969,820000,3,26,1,adjusted_type_specific_poisson,0.00894320495196033,0.00593991954160081,0.0125399202948559,0.363495562185596,0.276041416147802,0.470834966111799,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,26.5523755023702,17.6356211190128,37.2310233554273,1.43364890004468,0.615686934708725,2.68204945721551,0.552375502370232,0.433648900044683,No PCV -Massachusetts.post.PCV7,36,2969,820000,3,1,0,adjusted_type_specific_poisson,0.00064412580506712,7.86357629764616e-05,0.00182850525733069,0.363495562185596,0.276041416147802,0.470834966111799,0.000211384916000071,1.20317230766708e-06,0.00166520932006513,1.91240951524428,0.233469580277114,5.42883210901482,0.0901625094104256,0.000296374540941925,0.700284415414289,0.912409515244278,0.0901625094104256,No PCV -Massachusetts.post.PCV7,37,2969,820000,3,3,0,adjusted_type_specific_poisson,0.00128768025515235,0.000353618139578408,0.00280675616950626,0.363495562185596,0.276041416147802,0.470834966111799,0.000155201681937787,5.20169758717572e-06,0.000602123592537372,3.82312267754733,1.0498922564083,8.33325906726408,0.169365002275345,0.00459700115025023,0.721700995687298,0.823122677547332,0.169365002275345,No PCV -Massachusetts.post.PCV7,38,2969,820000,3,5,2,adjusted_type_specific_poisson,0.00205193012970651,0.000865325104796392,0.00376148694459967,0.363495562185596,0.276041416147802,0.470834966111799,0.00107630112860654,0.000517329118040196,0.00192400799311281,6.09218055509862,2.56915023614049,11.1678547385164,1.90291135706096,0.691100387261443,3.89881977812168,1.09218055509862,0.0970886429390423,No PCV -Massachusetts.post.PCV7,4,2969,820000,3,0,3,adjusted_type_specific_poisson,0.000781559313815827,0.000208180117485297,0.00174094093409302,0.363495562185596,0.276041416147802,0.470834966111799,0.00249105790199758,0.00143369758150515,0.00400799422771078,2.32044960271919,0.618086768813845,5.16885363332218,1.67589362206577,0.439655312598347,3.82818634564402,2.32044960271919,1.32410637793423,PCV7 -Massachusetts.post.PCV7,6A,2969,820000,3,27,12,adjusted_type_specific_poisson,0.011784750336116,0.00847305865274597,0.0156305452896393,0.363495562185596,0.276041416147802,0.470834966111799,0.000470534749603847,0.000335293276070173,0.000638312814574088,34.9889237479285,25.1565111400028,46.4070889649391,4.88921301196469,3.16706461456715,7.0928853731218,7.98892374792853,7.11078698803531,PCV13 -Massachusetts.post.PCV7,6B,2969,820000,3,8,2,adjusted_type_specific_poisson,0.00301163931446615,0.00149748170136023,0.00503439514547273,0.363495562185596,0.276041416147802,0.470834966111799,0.000770579380902745,0.000565085521465747,0.00101866271810419,8.94155712465001,4.44602317133851,14.9471191869085,2.0445093637905,0.981303173026474,3.5475433321735,0.941557124650011,0.0445093637905041,PCV7 -Massachusetts.post.PCV7,6C,2969,820000,3,65,1,adjusted_type_specific_poisson,0.0218949274914973,0.0169827995944033,0.0274031391409979,0.363495562185596,0.276041416147802,0.470834966111799,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,65.0060397222556,50.4219319957835,81.3599201096227,1.97028611656555,0.839048183044808,3.69252259542761,0.00603972225557925,0.970286116565548,No PCV -Massachusetts.post.PCV7,7C,2969,820000,3,5,1,adjusted_type_specific_poisson,0.0020955039498781,0.000826738533872324,0.00395166470285947,0.363495562185596,0.276041416147802,0.470834966111799,0.000430538003690001,0.000121592824190092,0.000973102091763221,6.22155122718809,2.45458670706693,11.7324925027898,0.777675831385358,0.16999720580235,2.00816810522539,1.22155122718809,0.222324168614642,No PCV -Massachusetts.post.PCV7,7F,2969,820000,3,21,28,adjusted_type_specific_poisson,0.00432030627375092,0.00285057140685511,0.00615339231291991,0.363495562185596,0.276041416147802,0.470834966111799,0.00997721126084835,0.00681051079664878,0.01416409744657,12.8269893267665,8.46334650695282,18.2694217770592,37.2334456839307,27.1437235476371,48.9274644977002,8.17301067323351,9.23344568393072,PCV10 -Massachusetts.post.PCV7,9A,2969,820000,3,1,0,adjusted_type_specific_poisson,0.000582568669164994,6.58942923208065e-05,0.00167990178675986,0.363495562185596,0.276041416147802,0.470834966111799,0.000693492945095352,1.08310516244248e-05,0.0036545591314838,1.72964637875087,0.195640153900474,4.98762840489002,0.270054447446812,0.00341273033697092,1.37395261993054,0.729646378750866,0.270054447446812,No PCV -Massachusetts.post.PCV7,9N,2969,820000,3,4,0,adjusted_type_specific_poisson,0.00141144524778809,0.000453638507797056,0.00290196554484512,0.363495562185596,0.276041416147802,0.470834966111799,0.00065486417300752,0.000292518419108024,0.00122095961399422,4.19058094068285,1.34685272964946,8.61593570264515,0.801063740677218,0.211842282033146,1.8941254570385,0.190580940682853,0.801063740677218,PPV23 -Massachusetts.post.PCV7,9V,2969,820000,3,2,0,adjusted_type_specific_poisson,0.000574341982854961,0.000115755713510683,0.00140219915171909,0.363495562185596,0.276041416147802,0.470834966111799,0.00259101673359874,0.00162148522659737,0.00391316735192488,1.70522134709638,0.343678713413218,4.16312928145397,1.29032131390311,0.260115461394211,3.14187829077447,0.294778652903622,1.29032131390311,PCV7 -Navajo.post.PCV7,1,6541,65048,6,8,22,adjusted_type_specific_poisson,0.00215445335201975,0.00135660898297346,0.0031471575275064,1,1,1,0.0206062908877376,0.0133467842050282,0.0309526551119594,14.0922793755612,8.87357935762939,20.5855573874193,16.8860909225689,10.9873412630996,24.19680575079,6.09227937556119,5.11390907743111,PCV10 -Navajo.post.PCV7,10A,6541,65048,6,85,0,adjusted_type_specific_poisson,0.0125513738284625,0.0100521012667918,0.01531423368735,1,1,1,0.000793695374669934,0.000513989148006867,0.00115253233769801,82.0985362119732,65.7507943860854,100.170402548957,3.87995042435775,2.43338206521105,5.76855346505389,2.90146378802682,3.87995042435775,PCV20 -Navajo.post.PCV7,10C,6541,65048,6,1,0,adjusted_type_specific_poisson,0.00028784960441872,3.28823136706134e-05,0.000818526055722309,1,1,1,0.00193953748370211,1.23456871707909e-06,0.0151225691911657,1.88282426250285,0.215083213719482,5.35397893047962,0.115545317221792,6.96807796975364e-05,1.01226022734389,0.882824262502846,0.115545317221792,No PCV -Navajo.post.PCV7,10F,6541,65048,6,25,0,adjusted_type_specific_poisson,0.00394916444351732,0.00258248444605095,0.00560037437800509,1,1,1,0.000113711965542455,1.15901196994602e-06,0.000833561695781898,25.8314846250468,16.8920307616193,36.6320488065313,0.169862689283875,0.00172042129641999,1.23856858251349,0.831484625046802,0.169862689283875,No PCV -Navajo.post.PCV7,11A,6541,65048,6,92,0,adjusted_type_specific_poisson,0.014145515182853,0.0114073504053572,0.0171584670445689,1,1,1,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,92.5258148110417,74.6154790014417,112.233532938525,0.473053393634348,0.223679533833037,0.838349514165928,0.525814811041656,0.473053393634348,PCV20 -Navajo.post.PCV7,12F,6541,65048,6,25,15,adjusted_type_specific_poisson,0.00433585787204586,0.00295649237769579,0.0059936382284332,1,1,1,0.00763701563010158,0.00413184393687895,0.0128667210227945,28.3608463410519,19.3384166425081,39.2043876521816,12.5953518782072,7.23666494785837,19.654429889869,3.36084634105194,2.40464812179281,PCV20 -Navajo.post.PCV7,14,6541,65048,6,4,0,adjusted_type_specific_poisson,0.000593797653721773,0.000193414900685224,0.00121492223200962,1,1,1,0.00486577684119951,0.00359593248342883,0.00641271837258626,3.88403045299412,1.26512686538205,7.9468063195749,1.12161036131843,0.361114863018252,2.33513407365949,0.115969547005882,1.12161036131843,PCV7 -Navajo.post.PCV7,15A,6541,65048,6,132,4,adjusted_type_specific_poisson,0.0203914367788849,0.0172093322840606,0.0238480240481186,1,1,1,0.000447893348168094,0.000276077603700969,0.000677854020290881,133.380387970686,112.566242470041,155.989925298744,3.55916821940331,2.1656394609072,5.45933624765173,1.38038797068623,0.440831780596691,No PCV -Navajo.post.PCV7,15B/C,6541,65048,6,124,2,adjusted_type_specific_poisson,0.018953754053017,0.0157955286916346,0.0224132593616553,1,1,1,0.000410284575081173,0.000285934443755961,0.000563977573171364,123.976505260784,103.318553171982,146.605129484587,3.03304880249113,2.03493755665747,4.2932886996237,0.0234947392160763,1.03304880249113,PCV20 -Navajo.post.PCV7,16F,6541,65048,6,83,1,adjusted_type_specific_poisson,0.012656933262282,0.0101383095452538,0.0154729509431127,1,1,1,0.000442387133406364,0.000231326668676358,0.000740352472096137,82.7890004685864,66.3146827355048,101.2085721189,2.18022253553783,1.11206594128243,3.72362671233093,0.210999531413634,1.18022253553783,No PCV -Navajo.post.PCV7,17F,6541,65048,6,96,1,adjusted_type_specific_poisson,0.0146333263209796,0.0119143586241625,0.0176279971244218,1,1,1,0.000400957354522875,0.000201346292292629,0.000689191021815353,95.7165874655274,77.9318197606467,115.304729190843,2.28555501784539,1.12147570143993,4.00579452598755,0.283412534472617,1.28555501784539,PPV23 -Navajo.post.PCV7,18C,6541,65048,6,1,0,adjusted_type_specific_poisson,0.000253521721800461,3.01478934735354e-05,0.000712807242710786,1,1,1,0.00341462550925104,0.0021814214974022,0.00511035484325696,1.65828558229681,0.197197371210395,4.66247217457125,0.335202665538578,0.0380057834097767,0.983060347545515,0.658285582296815,0.335202665538578,PCV7 -Navajo.post.PCV7,19A,6541,65048,6,208,29,adjusted_type_specific_poisson,0.0325900522310905,0.0285758625249283,0.0368350423761617,1,1,1,0.00193665997116141,0.00151058619668583,0.00243196471893208,213.171531643563,186.914716775556,240.938012182474,24.595654812257,18.9339080072033,31.089349384018,5.17153164356321,4.40434518774296,PCV13 -Navajo.post.PCV7,19F,6541,65048,6,35,1,adjusted_type_specific_poisson,0.00541101654818911,0.00380870766067593,0.00727355461730751,1,1,1,0.000752568056083617,0.000550123319373138,0.00100157805364369,35.3934592417049,24.9127568084812,47.5763207518084,1.58812322207385,0.99157861119118,2.36662170299827,0.393459241704946,0.588123222073852,PCV7 -Navajo.post.PCV7,20,6541,65048,6,1,0,adjusted_type_specific_poisson,0.000288866811818622,3.61824382063045e-05,0.000802629125420197,1,1,1,0.000957797173992484,0.000238388518107766,0.00247568343665466,1.88947781610561,0.236669328307437,5.24999710937351,0.10585518204951,0.00860343138196007,0.388889436353626,0.889477816105606,0.10585518204951,PPV23 -Navajo.post.PCV7,21,6541,65048,6,88,2,adjusted_type_specific_poisson,0.0137093700269878,0.011057167932006,0.0167002395385405,1,1,1,0.000234606065585659,0.00010602199615295,0.000423079520489989,89.6729893465275,72.3249354432514,109.236266821593,1.25280335628068,0.555637938514814,2.3084586888129,1.6729893465275,0.747196643719318,No PCV -Navajo.post.PCV7,22A,6541,65048,6,1,0,adjusted_type_specific_poisson,0.000289164248704307,3.33171413130484e-05,0.000828393793698421,1,1,1,0.00189124622795358,1.2573996172372e-06,0.0147541833751184,1.89142335077488,0.217927421328649,5.41852380458137,0.11285857089495,7.03341976445204e-05,0.995209167147475,0.891423350774875,0.11285857089495,No PCV -Navajo.post.PCV7,22F,6541,65048,6,134,4,adjusted_type_specific_poisson,0.0199308254760323,0.0167562119221193,0.0234170195961054,1,1,1,0.00111291794656347,0.000747288532056908,0.00157611065350571,130.367529438727,109.602382182582,153.170725178125,8.63714765078891,5.6990119456946,12.3640554344307,3.63247056127292,4.63714765078891,PCV15 -Navajo.post.PCV7,23A,6541,65048,6,89,1,adjusted_type_specific_poisson,0.0137604231588776,0.0111081199283202,0.016699555227399,1,1,1,0.00017858253466746,0.000100358645533425,0.000284446850590249,90.0069278822184,72.6582124511424,109.231790742417,0.958161662851184,0.520872812319363,1.56998598857671,1.00692788221836,0.0418383371488158,No PCV -Navajo.post.PCV7,23B,6541,65048,6,137,3,adjusted_type_specific_poisson,0.0211970905587625,0.0178472589811741,0.024781104002124,1,1,1,0.000290469676688038,0.000174295346379655,0.000444118199022155,138.650169344865,116.73892099586,162.093201277893,2.40043191704372,1.40929031551066,3.72831481025927,1.65016934486536,0.599568082956278,No PCV -Navajo.post.PCV7,27,6541,65048,6,1,0,adjusted_type_specific_poisson,0.000225938066146147,2.54504566552223e-05,0.00065016378469232,1,1,1,0.00667616951433804,0.00152734556090641,0.0197265487315555,1.47786089066195,0.166471436981809,4.25272131567247,0.522797856780803,0.0453811640443525,1.79409966702219,0.477860890661947,0.522797856780803,No PCV -Navajo.post.PCV7,3,6541,65048,6,73,10,adjusted_type_specific_poisson,0.011372781569623,0.00908874412887623,0.0138988087817157,1,1,1,0.00214630789735218,0.00150111695338643,0.00296037810122135,74.3893642469041,59.4494753469794,90.9121082412025,9.49526162877045,6.43780611354691,13.352974927991,1.38936424690414,0.50473837122955,PCV13 -Navajo.post.PCV7,31,6541,65048,6,50,1,adjusted_type_specific_poisson,0.00770131537419871,0.00574111617913258,0.00993428320797413,1,1,1,0.000529235275657269,0.000187950733188048,0.00110145716265855,50.3743038626337,37.5526409277062,64.9801464633588,1.58069541689786,0.549489662440543,3.29660129101757,0.374303862633745,0.580695416897858,No PCV -Navajo.post.PCV7,33A,6541,65048,6,1,0,adjusted_type_specific_poisson,0.000302698556632764,3.6812161409432e-05,0.000846494980058495,1,1,1,0.000126887088118296,1.17148310590837e-06,0.000937616322945586,1.97995125893491,0.240788347779095,5.53692366456262,0.0144032435674287,5.66068809484561e-05,0.115081603840123,0.97995125893491,0.0144032435674287,No PCV -Navajo.post.PCV7,33F,6541,65048,6,60,2,adjusted_type_specific_poisson,0.00884917613579362,0.00677724385318248,0.0112142439493447,1,1,1,0.00147980242560294,0.000904545029211608,0.00226255226693128,57.882461104226,44.3299520436666,73.3523696726634,5.08609788237812,2.9871748365083,7.91455099060181,2.11753889577395,3.08609788237812,PCV15 -Navajo.post.PCV7,34,6541,65048,6,89,1,adjusted_type_specific_poisson,0.0138012828613614,0.0111496660466378,0.016708508379663,1,1,1,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,90.2741911961647,72.9299656110576,109.290353311375,0.635171669390259,0.124482882580898,1.60049742066413,1.27419119616471,0.364828330609741,No PCV -Navajo.post.PCV7,35A,6541,65048,6,55,0,adjusted_type_specific_poisson,0.00853294477722634,0.00644902104452477,0.0109008701393086,1,1,1,5.97046750229502e-05,1.13639832230425e-06,0.000418924812601197,55.8139917878375,42.1830466522365,71.3025915812173,0.19590806515054,0.00372200844679343,1.35496154810937,0.813991787837473,0.19590806515054,No PCV -Navajo.post.PCV7,35B,6541,65048,6,137,2,adjusted_type_specific_poisson,0.0212102396748429,0.0179136802136745,0.0247522691818208,1,1,1,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,138.736177713147,117.173382277645,161.90459271829,1.19421391142751,0.550417269963786,2.15484727209375,1.73617771314744,0.805786088572491,No PCV -Navajo.post.PCV7,35F,6541,65048,6,58,0,adjusted_type_specific_poisson,0.00891815457023051,0.00677090219903045,0.0113473436213818,1,1,1,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,58.3336490438778,44.2884712838582,74.2229746274583,0.634208072924585,0.279913547512068,1.18141418625275,0.333649043877791,0.634208072924585,No PCV -Navajo.post.PCV7,37,6541,65048,6,10,0,adjusted_type_specific_poisson,0.00166469711320155,0.00083208652074687,0.00277547073395191,1,1,1,0.000155201681937787,5.20169758717572e-06,0.000602123592537372,10.8887838174513,5.44267793220527,18.1543540707794,0.0999911919396776,0.00311304859525081,0.413094243232855,0.888783817451309,0.0999911919396776,No PCV -Navajo.post.PCV7,38,6541,65048,6,32,1,adjusted_type_specific_poisson,0.00488534665115869,0.00336434739010164,0.00669261775452588,1,1,1,0.00107630112860654,0.000517329118040196,0.00192400799311281,31.955052445229,22.0061962786548,43.7764127323538,2.03791505156626,0.924079399955555,3.77682548430311,0.0449475547709888,1.03791505156626,No PCV -Navajo.post.PCV7,4,6541,65048,6,5,0,adjusted_type_specific_poisson,0.00079853503741368,0.000290730057300208,0.00156092784903007,1,1,1,0.00249105790199758,0.00143369758150515,0.00400799422771078,5.22321767972288,1.90166530480066,10.2100290605057,0.76959909080269,0.249725443890353,1.66493580206818,0.223217679722878,0.76959909080269,PCV7 -Navajo.post.PCV7,5,6541,65048,6,2,0,adjusted_type_specific_poisson,0.000305415257093755,6.10051296467693e-05,0.000751659099044585,1,1,1,0.00898185496955944,0.00375244500011871,0.0188069207217874,1.99772119665025,0.399034553019518,4.91660216685063,1.01216518113872,0.181705830504561,2.69078753380824,0.00227880334974717,1.01216518113872,PCV10 -Navajo.post.PCV7,6B,6541,65048,6,4,0,adjusted_type_specific_poisson,0.000730943545510663,0.000241041798214904,0.00148911268024751,1,1,1,0.000770579380902745,0.000565085521465747,0.00101866271810419,4.78110173118525,1.57665440212368,9.74028604149899,0.219595930000471,0.069842995363868,0.466093070310259,0.781101731185247,0.219595930000471,PCV7 -Navajo.post.PCV7,7C,6541,65048,6,60,1,adjusted_type_specific_poisson,0.0092444102281289,0.00707135551349146,0.0116969090079583,1,1,1,0.000430538003690001,0.000121592824190092,0.000973102091763221,60.4676873021911,46.2537364137476,76.5094818210556,1.54266902534144,0.432273112009657,3.4968924696375,0.467687302191109,0.542669025341435,No PCV -Navajo.post.PCV7,7F,6541,65048,6,13,24,adjusted_type_specific_poisson,0.00365614924850027,0.00251837834868668,0.00498457844602716,1,1,1,0.00997721126084835,0.00681051079664878,0.01416409744657,23.9148722344403,16.4727127787596,32.6041276154637,14.0567472030134,9.2119575180677,20.1585728942684,10.9148722344403,9.94325279698657,PCV10 -Navajo.post.PCV7,8,6541,65048,6,11,1,adjusted_type_specific_poisson,0.00174070704852655,0.000917498215856096,0.00282961412498566,1,1,1,0.00244545634969096,0.00123914949735586,0.00432306004960451,11.3859648044122,6.00135582991472,18.5085059915312,1.63932705064803,0.676044797383313,3.20852208779093,0.385964804412176,0.639327050648029,PCV20 -Navajo.post.PCV7,9N,6541,65048,6,9,0,adjusted_type_specific_poisson,0.00147454585141215,0.000707145359221629,0.00251881524532174,1,1,1,0.00065486417300752,0.000292518419108024,0.00122095961399422,9.64500441408686,4.62543779466867,16.4755705196495,0.374976271414136,0.126853770207682,0.826625605038527,0.645004414086859,0.374976271414136,PPV23 -Navajo.post.PCV7,9V,6541,65048,6,7,0,adjusted_type_specific_poisson,0.00105819786839506,0.000449126911391975,0.00192696609597318,1,1,1,0.00259101673359874,0.00162148522659737,0.00391316735192488,6.92167225717211,2.93773912741491,12.6042852337606,1.06239642761799,0.414189485462935,2.09796744239632,0.0783277428278861,1.06239642761799,PCV7 -Netherlands.post.PCV10,1,659,222671,4,3,3,adjusted_type_specific_poisson,0.00252996141834254,0.000915899883836995,0.00516470873824804,0.122134469446819,0.0801536374842461,0.178204157790169,0.0206062908877376,0.0133467842050282,0.0309526551119594,1.66724457468773,0.60357802344858,3.40354305850546,5.33412052173583,2.09239292524415,10.1228787135321,1.33275542531227,2.33412052173583,PCV10 -Netherlands.post.PCV10,10A,659,222671,4,13,4,adjusted_type_specific_poisson,0.0240243081432562,0.0142564908262443,0.0361474403138935,0.122134469446819,0.0801536374842461,0.178204157790169,0.000793695374669934,0.000513989148006867,0.00115253233769801,15.8320190664058,9.39502745449496,23.8211631668558,2.04068325894597,0.996058750582674,3.60244262834719,2.83201906640581,1.95931674105403,PCV20 -Netherlands.post.PCV10,10B,659,222671,4,2,1,adjusted_type_specific_poisson,0.00546204927974746,0.00147463229943801,0.0120816479086436,0.122134469446819,0.0801536374842461,0.178204157790169,0.000696632980137251,9.61989918783685e-05,0.00234483425439832,3.59949047535357,0.97178268532965,7.9618059717961,0.381523412963239,0.0379218696840355,1.35389888712577,1.59949047535357,0.618476587036761,No PCV -Netherlands.post.PCV10,11A,659,222671,4,31,0,adjusted_type_specific_poisson,0.0478437358180965,0.0329925498779913,0.0655579586227591,0.122134469446819,0.0801536374842461,0.178204157790169,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,31.5290219041256,21.7420903695963,43.2026947323982,0.440281261439494,0.187473580641163,0.843007249288377,0.529021904125585,0.440281261439494,PCV20 -Netherlands.post.PCV10,14,659,222671,4,0,1,adjusted_type_specific_poisson,0.00170324295661943,0.000208713036068678,0.00480062697779309,0.122134469446819,0.0801536374842461,0.178204157790169,0.00486577684119951,0.00359593248342883,0.00641271837258626,1.1224371084122,0.137541890769259,3.16361317836564,0.876452074591469,0.106124835737252,2.49046689213414,1.1224371084122,0.123547925408531,PCV7 -Netherlands.post.PCV10,15A,659,222671,4,8,0,adjusted_type_specific_poisson,0.012685606243344,0.00586175133315337,0.0220008430793742,0.122134469446819,0.0801536374842461,0.178204157790169,0.000447893348168094,0.000276077603700969,0.000677854020290881,8.35981451436367,3.86289412854807,14.4985555893076,0.608859194658962,0.2347929275374,1.22561646060292,0.359814514363668,0.608859194658962,No PCV -Netherlands.post.PCV10,15B/C,659,222671,4,28,2,adjusted_type_specific_poisson,0.0440419095813346,0.0302011145652251,0.0603441626700796,0.122134469446819,0.0801536374842461,0.178204157790169,0.000410284575081173,0.000285934443755961,0.000563977573171364,29.0236184140995,19.9025344984833,39.7668031995824,1.93954987915393,1.07801579096342,3.16813474506195,1.02361841409953,0.0604501208460742,PCV20 -Netherlands.post.PCV10,15F,659,222671,4,1,0,adjusted_type_specific_poisson,0.00291204433920908,0.000353477116160455,0.0081057617240368,0.122134469446819,0.0801536374842461,0.178204157790169,0.000241837303648991,2.36364376734738e-05,0.000792155722410316,1.91903721953878,0.23294141954974,5.34169697614025,0.0739120023362277,0.00297916210617817,0.326982241059462,0.919037219538783,0.0739120023362277,No PCV -Netherlands.post.PCV10,16F,659,222671,4,10,1,adjusted_type_specific_poisson,0.0169575178697206,0.00878752765884312,0.0277921891231571,0.122134469446819,0.0801536374842461,0.178204157790169,0.000442387133406364,0.000231326668676358,0.000740352472096137,11.1750042761459,5.79098072717762,18.3150526321606,0.801923487656072,0.312580496528859,1.62843477133622,1.1750042761459,0.198076512343928,No PCV -Netherlands.post.PCV10,17F,659,222671,4,6,1,adjusted_type_specific_poisson,0.0113621889313696,0.00492133310935989,0.0202917172802985,0.122134469446819,0.0801536374842461,0.178204157790169,0.000400957354522875,0.000201346292292629,0.000689191021815353,7.48768250577259,3.24315851906817,13.3722416877167,0.487735639301503,0.159889103225283,1.06684357006721,1.48768250577259,0.512264360698497,PPV23 -Netherlands.post.PCV10,18C,659,222671,4,0,1,adjusted_type_specific_poisson,0.00196521056777604,0.000242106398187291,0.00545076599633764,0.122134469446819,0.0801536374842461,0.178204157790169,0.00341462550925104,0.0021814214974022,0.00511035484325696,1.29507376416441,0.159548116405425,3.59205479158651,0.705479067234677,0.0843304692819337,2.02608959582839,1.29507376416441,0.294520932765323,PCV7 -Netherlands.post.PCV10,19A,659,222671,4,41,5,adjusted_type_specific_poisson,0.0545480689150914,0.0396184005910808,0.0716742917318431,0.122134469446819,0.0801536374842461,0.178204157790169,0.00193665997116141,0.00151058619668583,0.00243196471893208,35.9471774150452,26.1085259895223,47.2333582512846,11.2834322101921,7.34057154288018,16.3671723280085,5.05282258495476,6.28343221019206,PCV13 -Netherlands.post.PCV10,19F,659,222671,4,5,1,adjusted_type_specific_poisson,0.00944228387880996,0.00383017373762372,0.0175864660643415,0.122134469446819,0.0801536374842461,0.178204157790169,0.000752568056083617,0.000550123319373138,0.00100157805364369,6.22246507613576,2.52408449309403,11.589481136401,0.761524528880483,0.282643097961985,1.53673208163139,1.22246507613576,0.238475471119517,PCV7 -Netherlands.post.PCV10,21,659,222671,4,14,0,adjusted_type_specific_poisson,0.0219053308599092,0.0124235913391837,0.034060593023538,0.122134469446819,0.0801536374842461,0.178204157790169,0.000234606065585659,0.00010602199615295,0.000423079520489989,14.4356130366801,8.18714669252207,22.4459308025115,0.549524279988923,0.200610497763906,1.141633174143,0.435613036680131,0.549524279988923,No PCV -Netherlands.post.PCV10,22F,659,222671,4,5,2,adjusted_type_specific_poisson,0.0102119892221891,0.00437006367063517,0.0184772582587724,0.122134469446819,0.0801536374842461,0.178204157790169,0.00111291794656347,0.000747288532056908,0.00157611065350571,6.72970089742259,2.87987195894857,12.176513192531,1.21347330823338,0.472703741730946,2.3899005922324,1.72970089742259,0.786526691766622,PCV15 -Netherlands.post.PCV10,23A,659,222671,4,18,1,adjusted_type_specific_poisson,0.0293760719366018,0.0180557940770837,0.0434696979766398,0.122134469446819,0.0801536374842461,0.178204157790169,0.00017858253466746,0.000100358645533425,0.000284446850590249,19.3588314062206,11.8987682967981,28.6465309666056,0.563426569194879,0.248724048410834,1.06095307604299,1.35883140622056,0.436573430805121,No PCV -Netherlands.post.PCV10,23B,659,222671,4,45,3,adjusted_type_specific_poisson,0.0707211136217339,0.0530999021769693,0.0909860386777498,0.122134469446819,0.0801536374842461,0.178204157790169,0.000290469676688038,0.000174295346379655,0.000444118199022155,46.6052138767226,34.9928355346227,59.9597994886371,2.20027166494953,1.1691888052075,3.68176456158949,1.60521387672264,0.799728335050474,No PCV -Netherlands.post.PCV10,23F,659,222671,4,0,1,adjusted_type_specific_poisson,0.00269191814124184,0.000333977161479059,0.00742261716227209,0.122134469446819,0.0801536374842461,0.178204157790169,0.00077564137009531,0.000556479798610777,0.00105106918760042,1.77397405507838,0.2200909494147,4.89150470993731,0.223423167906638,0.0260011223179897,0.637465792879206,1.77397405507838,0.776576832093362,PCV7 -Netherlands.post.PCV10,24F,659,222671,4,5,2,adjusted_type_specific_poisson,0.00825350510871364,0.00342916278724215,0.0153278762275746,0.122134469446819,0.0801536374842461,0.178204157790169,0.00296592942741409,0.00168198604203905,0.00494246465975427,5.43905986664229,2.25981827679257,10.1010704339716,2.55404491388166,0.984655092244678,5.10462126736174,0.439059866642287,0.554044913881664,No PCV -Netherlands.post.PCV10,27,659,222671,4,0,2,adjusted_type_specific_poisson,0.00241228249357526,0.00042208037610329,0.00635990388949691,0.122134469446819,0.0801536374842461,0.178204157790169,0.00667616951433804,0.00152734556090641,0.0197265487315555,1.5896941632661,0.278150967852068,4.19117666317847,1.40509996332952,0.234499038828899,3.7864178317169,1.5896941632661,0.594900036670476,No PCV -Netherlands.post.PCV10,3,659,222671,4,2,5,adjusted_type_specific_poisson,0.00897601571307675,0.00389661646936413,0.0162248632926843,0.122134469446819,0.0801536374842461,0.178204157790169,0.00214630789735218,0.00150111695338643,0.00296037810122135,5.91519435491758,2.56787025331096,10.6921849098789,2.04801707643235,0.831533500839165,3.92513019605084,3.91519435491758,2.95198292356765,PCV13 -Netherlands.post.PCV10,31,659,222671,4,2,0,adjusted_type_specific_poisson,0.00416656074902128,0.000850295643875637,0.0100053267978912,0.122134469446819,0.0801536374842461,0.178204157790169,0.000529235275657269,0.000187950733188048,0.00110145716265855,2.74576353360503,0.560344829314045,6.59351035981027,0.234671407805913,0.0341645936974838,0.710451267690984,0.745763533605025,0.234671407805913,No PCV -Netherlands.post.PCV10,33A,659,222671,4,1,0,adjusted_type_specific_poisson,0.00297515046989946,0.000374850066848229,0.00829392603177555,0.122134469446819,0.0801536374842461,0.178204157790169,0.000126887088118296,1.17148310590837e-06,0.000937616322945586,1.96062415966375,0.247026194052983,5.46569725494009,0.036841715595035,0.000146272844704459,0.291456099729224,0.960624159663747,0.036841715595035,No PCV -Netherlands.post.PCV10,33F,659,222671,4,7,2,adjusted_type_specific_poisson,0.0122289762286197,0.00585636519876575,0.0210896968443061,0.122134469446819,0.0801536374842461,0.178204157790169,0.00147980242560294,0.000904545029211608,0.00226255226693128,8.05889533466041,3.85934466598663,13.8981102203977,1.92230152370851,0.802141079228127,3.69705093808871,1.05889533466041,0.0776984762914947,PCV15 -Netherlands.post.PCV10,34,659,222671,4,0,1,adjusted_type_specific_poisson,0.00296227877653339,0.000362039395579045,0.00822930149884784,0.122134469446819,0.0801536374842461,0.178204157790169,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,1.95214171373551,0.238583961686591,5.42310968774073,0.0374642419600982,0.00245149480442228,0.143944099868919,1.95214171373551,0.962535758039902,No PCV -Netherlands.post.PCV10,35B,659,222671,4,12,0,adjusted_type_specific_poisson,0.0191657477279943,0.0103265232612171,0.0305571743197007,0.122134469446819,0.0801536374842461,0.178204157790169,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,12.6302277527483,6.80517882914205,20.1371778766828,0.2972552084785,0.1062319697448,0.632706567576838,0.630227752748254,0.2972552084785,No PCV -Netherlands.post.PCV10,35F,659,222671,4,12,0,adjusted_type_specific_poisson,0.0191256104578247,0.0102151539336491,0.0306454673223802,0.122134469446819,0.0801536374842461,0.178204157790169,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,12.6037772917065,6.73178644227474,20.1953629654486,0.373116941489843,0.134326421289342,0.787623267159788,0.603777291706479,0.373116941489843,No PCV -Netherlands.post.PCV10,37,659,222671,4,1,0,adjusted_type_specific_poisson,0.00295427567011481,0.000363178359697261,0.00816993696345602,0.122134469446819,0.0801536374842461,0.178204157790169,0.000155201681937787,5.20169758717572e-06,0.000602123592537372,1.94686766660566,0.239334539040495,5.38398845891752,0.0475642509151995,0.000847501062120112,0.232430284034261,0.946867666605657,0.0475642509151995,No PCV -Netherlands.post.PCV10,38,659,222671,4,4,0,adjusted_type_specific_poisson,0.00645793589393307,0.00212357674211645,0.0133380583535254,0.122134469446819,0.0801536374842461,0.178204157790169,0.00107630112860654,0.000517329118040196,0.00192400799311281,4.25577975410189,1.39943707305474,8.78978045497321,0.73433120908495,0.191104882453552,1.76953270425509,0.255779754101892,0.73433120908495,No PCV -Netherlands.post.PCV10,4,659,222671,4,0,1,adjusted_type_specific_poisson,0.00216730439029748,0.000253893541937959,0.00612140925125666,0.122134469446819,0.0801536374842461,0.178204157790169,0.00249105790199758,0.00143369758150515,0.00400799422771078,1.42825359320604,0.167315844137115,4.03400869657814,0.565826096794846,0.0626677315146442,1.66990083178807,1.42825359320604,0.434173903205154,PCV7 -Netherlands.post.PCV10,6A,659,222671,4,2,0,adjusted_type_specific_poisson,0.00421639031204755,0.000866380761256849,0.0101523036325062,0.122134469446819,0.0801536374842461,0.178204157790169,0.000470534749603847,0.000335293276070173,0.000638312814574088,2.77860121563934,0.570944921668264,6.69036809382161,0.213141919867762,0.0402952374456898,0.545319450387713,0.778601215639338,0.213141919867762,PCV13 -Netherlands.post.PCV10,6C,659,222671,4,44,2,adjusted_type_specific_poisson,0.0698403695705401,0.051664557860391,0.0901362990401904,0.122134469446819,0.0801536374842461,0.178204157790169,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,46.0248035469859,34.0469436299977,59.3998210674855,0.76542412723624,0.296482513413029,1.51985525955005,2.0248035469859,1.23457587276376,No PCV -Netherlands.post.PCV10,7F,659,222671,4,3,2,adjusted_type_specific_poisson,0.00353929687663666,0.00124742327370926,0.00714716822068099,0.122134469446819,0.0801536374842461,0.178204157790169,0.00997721126084835,0.00681051079664878,0.01416409744657,2.33239664170356,0.822051937374405,4.70998385742877,3.67978384751643,1.34734406158121,7.29562286605682,0.667603358296439,1.67978384751643,PCV10 -Netherlands.post.PCV10,8,659,222671,4,0,2,adjusted_type_specific_poisson,0.00327424915888894,0.000651889881021638,0.0079828743378762,0.122134469446819,0.0801536374842461,0.178204157790169,0.00244545634969096,0.00123914949735586,0.00432306004960451,2.15773019570781,0.429595431593259,5.26071418866042,0.834780975634836,0.149742587005363,2.17692995019491,2.15773019570781,1.16521902436516,PCV20 -Netherlands.post.PCV10,9N,659,222671,4,3,0,adjusted_type_specific_poisson,0.00546873124277232,0.00154315590808867,0.0119354771367881,0.122134469446819,0.0801536374842461,0.178204157790169,0.00065486417300752,0.000292518419108024,0.00122095961399422,3.60389388898696,1.01693974343043,7.86547943314339,0.379469105692146,0.0829185953229148,0.989249818260498,0.603893888986958,0.379469105692146,PPV23 -Netherlands.post.PCV10,9V,659,222671,4,0,1,adjusted_type_specific_poisson,0.0021426749606551,0.000252490091513516,0.00604249252482223,0.122134469446819,0.0801536374842461,0.178204157790169,0.00259101673359874,0.00162148522659737,0.00391316735192488,1.41202279907171,0.166390970307407,3.98200257385785,0.586249317197049,0.066713798920316,1.72354974794495,1.41202279907171,0.413750682802951,PCV7 -Netherlands.post.PCV7,1,660,232251,4,2,9,adjusted_type_specific_poisson,0.00444454487853168,0.00208034535778955,0.00795868399366428,0.112358990603774,0.0781814563989282,0.155318386005972,0.0206062908877376,0.0133467842050282,0.0309526551119594,2.93339961983091,1.37302793614111,5.25273143581842,9.06888049633947,4.63782364319781,15.0866309127616,0.933399619830906,0.0688804963394709,PCV10 -Netherlands.post.PCV7,10A,660,232251,4,20,8,adjusted_type_specific_poisson,0.0387820966083289,0.0260081470829844,0.054093264075667,0.112358990603774,0.0781814563989282,0.155318386005972,0.000793695374669934,0.000513989148006867,0.00115253233769801,25.5961837614971,17.1653770747697,35.7015542899402,3.16173541370356,1.74569545449016,5.13625872360714,5.59618376149708,4.83826458629644,PCV20 -Netherlands.post.PCV7,11A,660,232251,4,36,0,adjusted_type_specific_poisson,0.0551939394527347,0.0391305756364665,0.0739692200506276,0.112358990603774,0.0781814563989282,0.155318386005972,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,36.4280000388049,25.8261799200679,48.8196852334142,0.488056807970632,0.212573495785877,0.919817070270094,0.428000038804932,0.488056807970632,PCV20 -Netherlands.post.PCV7,12F,660,232251,4,1,0,adjusted_type_specific_poisson,0.00142028744524004,0.000165731536363795,0.0041667765973966,0.112358990603774,0.0781814563989282,0.155318386005972,0.00763701563010158,0.00413184393687895,0.0128667210227945,0.937389713858424,0.109382814000105,2.75007255428176,1.06663112179304,0.123501123319275,3.0854522218447,0.0626102861415756,1.06663112179304,PCV20 -Netherlands.post.PCV7,14,660,232251,4,2,0,adjusted_type_specific_poisson,0.00259568893158782,0.000525622386805784,0.00635217814764103,0.112358990603774,0.0781814563989282,0.155318386005972,0.00486577684119951,0.00359593248342883,0.00641271837258626,1.71315469484796,0.346910775291817,4.19243757744308,1.28602343662571,0.262292981497455,3.16030371539527,0.286845305152036,1.28602343662571,PCV7 -Netherlands.post.PCV7,15A,660,232251,4,2,2,adjusted_type_specific_poisson,0.00703935641399061,0.00229057823599408,0.0142493560403178,0.112358990603774,0.0781814563989282,0.155318386005972,0.000447893348168094,0.000276077603700969,0.000677854020290881,4.6459752332338,1.51178163575609,9.40457498660978,0.32476790274289,0.0926413152922117,0.729177269693356,2.6459752332338,1.67523209725711,No PCV -Netherlands.post.PCV7,15B/C,660,232251,4,29,2,adjusted_type_specific_poisson,0.0454480735851004,0.0310975918764717,0.0623279890740584,0.112358990603774,0.0781814563989282,0.155318386005972,0.000410284575081173,0.000285934443755961,0.000563977573171364,29.9957285661663,20.5244106384713,41.1364727888786,1.92189987884458,1.11217796834049,3.04617594032394,0.99572856616626,0.0781001211554182,PCV20 -Netherlands.post.PCV7,16F,660,232251,4,12,3,adjusted_type_specific_poisson,0.0225150951302416,0.0129039644721637,0.034722935363319,0.112358990603774,0.0781814563989282,0.155318386005972,0.000442387133406364,0.000231326668676358,0.000740352472096137,14.8599627859594,8.51661655162802,22.9171373397905,1.0215291247824,0.433807631959426,1.95106997646203,2.85996278595945,1.9784708752176,No PCV -Netherlands.post.PCV7,17F,660,232251,4,9,2,adjusted_type_specific_poisson,0.0170077020184687,0.0088185060849312,0.027725256561861,0.112358990603774,0.0781814563989282,0.155318386005972,0.000400957354522875,0.000201346292292629,0.000689191021815353,11.2250833321893,5.82021401605459,18.2986693308283,0.701483448008441,0.263432964773397,1.43908751158862,2.22508333218932,1.29851655199156,PPV23 -Netherlands.post.PCV7,18C,660,232251,4,2,2,adjusted_type_specific_poisson,0.00496381596631812,0.0015865785509548,0.0102472871789192,0.112358990603774,0.0781814563989282,0.155318386005972,0.00341462550925104,0.0021814214974022,0.00511035484325696,3.27611853776996,1.04714184363017,6.76320953808665,1.71724980727678,0.531398794589593,3.69829870578083,1.27611853776996,0.282750192723219,PCV7 -Netherlands.post.PCV7,19A,660,232251,4,68,10,adjusted_type_specific_poisson,0.0926943990179901,0.0733520771966075,0.114293776909533,0.112358990603774,0.0781814563989282,0.155318386005972,0.00193665997116141,0.00151058619668583,0.00243196471893208,61.1783033518735,48.4123709497609,75.433892760292,18.442254620432,13.1522344290007,24.9276619045258,6.82169664812655,8.44225462043199,PCV13 -Netherlands.post.PCV7,19F,660,232251,4,8,1,adjusted_type_specific_poisson,0.0135285215967954,0.00657656315617831,0.0230590068843047,0.112358990603774,0.0781814563989282,0.155318386005972,0.000752568056083617,0.000550123319373138,0.00100157805364369,8.92882425388497,4.34053168307768,15.2189445436411,1.04814217382024,0.464284743734792,1.93075053928284,0.928824253884972,0.0481421738202437,PCV7 -Netherlands.post.PCV7,21,660,232251,4,16,0,adjusted_type_specific_poisson,0.0247769410593513,0.0144991272916422,0.0377076093066103,0.112358990603774,0.0781814563989282,0.155318386005972,0.000234606065585659,0.00010602199615295,0.000423079520489989,16.3527810991718,9.56942401248385,24.8870221423628,0.598077546750752,0.227947057230206,1.23935065867044,0.352781099171839,0.598077546750752,No PCV -Netherlands.post.PCV7,22F,660,232251,4,7,4,adjusted_type_specific_poisson,0.0154007288157172,0.00801686041768578,0.0252451507842905,0.112358990603774,0.0781814563989282,0.155318386005972,0.00111291794656347,0.000747288532056908,0.00157611065350571,10.1644810183733,5.29112787567261,16.6617995176317,1.76025440054602,0.821079399213094,3.17655836876606,3.16448101837333,2.23974559945398,PCV15 -Netherlands.post.PCV7,23A,660,232251,4,11,0,adjusted_type_specific_poisson,0.0176396084630788,0.00909471900323962,0.0289825936607962,0.112358990603774,0.0781814563989282,0.155318386005972,0.00017858253466746,0.000100358645533425,0.000284446850590249,11.642141585632,6.00251454213815,19.1285118161255,0.325033484228538,0.13017023395553,0.642670745218072,0.642141585631995,0.325033484228538,No PCV -Netherlands.post.PCV7,23B,660,232251,4,24,1,adjusted_type_specific_poisson,0.0375852080352191,0.0246333090821808,0.0532015694857066,0.112358990603774,0.0781814563989282,0.155318386005972,0.000290469676688038,0.000174295346379655,0.000444118199022155,24.8062373032446,16.2579839942393,35.1130358605664,1.12520739617096,0.564369568846618,1.96660698315881,0.806237303244618,0.125207396170963,No PCV -Netherlands.post.PCV7,23F,660,232251,4,2,0,adjusted_type_specific_poisson,0.00404387273726329,0.000858577289426899,0.00971464547657516,0.112358990603774,0.0781814563989282,0.155318386005972,0.00077564137009531,0.000556479798610777,0.00105106918760042,2.66895600659377,0.566661011021753,6.4116660145396,0.322285099149872,0.0641774524778867,0.798280102361544,0.66895600659377,0.322285099149872,PCV7 -Netherlands.post.PCV7,24B,660,232251,4,0,1,adjusted_type_specific_poisson,0.00186957816224674,0.000155875816367087,0.00590476251478796,0.112358990603774,0.0781814563989282,0.155318386005972,0.00712047825808381,0.000499379415524034,0.0345762945937344,1.23392158708285,0.102878038802277,3.89714325976006,0.75903840525031,0.0507973559225125,2.77991899574991,1.23392158708285,0.24096159474969,No PCV -Netherlands.post.PCV7,24F,660,232251,4,3,1,adjusted_type_specific_poisson,0.0052141494831856,0.00167856718994677,0.0108713630513198,0.112358990603774,0.0781814563989282,0.155318386005972,0.00296592942741409,0.00168198604203905,0.00494246465975427,3.44133865890249,1.10785434536487,7.17509961387105,1.55565347733699,0.471886431399263,3.43904597296704,0.441338658902493,0.555653477336989,No PCV -Netherlands.post.PCV7,27,660,232251,4,0,3,adjusted_type_specific_poisson,0.003260679832258,0.000721122922122132,0.00799086453194145,0.112358990603774,0.0781814563989282,0.155318386005972,0.00667616951433804,0.00152734556090641,0.0197265487315555,2.15204868929028,0.475941128600607,5.27397059108136,1.84299967618759,0.376488792387914,4.68955021650543,2.15204868929028,1.15700032381241,No PCV -Netherlands.post.PCV7,3,660,232251,4,8,3,adjusted_type_specific_poisson,0.0135649763874858,0.00699653426058107,0.0223918016560736,0.112358990603774,0.0781814563989282,0.155318386005972,0.00214630789735218,0.00150111695338643,0.00296037810122135,8.95288441574062,4.6177126119835,14.7785890930086,2.97862924157246,1.43175146029397,5.24967517131214,0.952884415740616,0.0213707584275382,PCV13 -Netherlands.post.PCV7,31,660,232251,4,1,0,adjusted_type_specific_poisson,0.00279128854746451,0.000334556352198295,0.00774594687352803,0.112358990603774,0.0781814563989282,0.155318386005972,0.000529235275657269,0.000187950733188048,0.00110145716265855,1.84225044132658,0.220807192450875,5.1123249365285,0.151013735587853,0.0135455907555453,0.510830818006374,0.842250441326576,0.151013735587853,No PCV -Netherlands.post.PCV7,33A,660,232251,4,2,0,adjusted_type_specific_poisson,0.00446621158428296,0.000930466770899854,0.010649129244572,0.112358990603774,0.0781814563989282,0.155318386005972,0.000126887088118296,1.17148310590837e-06,0.000937616322945586,2.94769964562675,0.614108068793904,7.02842530141749,0.0531369574741348,0.000298159775936397,0.403070176028797,0.947699645626755,0.0531369574741348,No PCV -Netherlands.post.PCV7,33F,660,232251,4,7,1,adjusted_type_specific_poisson,0.0110872707070536,0.00498650074583968,0.0196325215877081,0.112358990603774,0.0781814563989282,0.155318386005972,0.00147980242560294,0.000904545029211608,0.00226255226693128,7.31759866665539,3.29109049225419,12.9574642478873,1.67518963607396,0.670808605276191,3.27119909479531,0.317598666655391,0.675189636073959,PCV15 -Netherlands.post.PCV7,35B,660,232251,4,9,0,adjusted_type_specific_poisson,0.0148006474674876,0.00713851039275746,0.0250821991417735,0.112358990603774,0.0781814563989282,0.155318386005972,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,9.76842732854184,4.71141685921993,16.5542514335705,0.22024522533283,0.0747547914248705,0.479724486408113,0.768427328541838,0.22024522533283,No PCV -Netherlands.post.PCV7,35F,660,232251,4,17,2,adjusted_type_specific_poisson,0.0293109095418631,0.0179314339440801,0.0432140245141148,0.112358990603774,0.0781814563989282,0.155318386005972,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,19.3452002976296,11.8347464030929,28.5212561793158,0.549616273440067,0.21812824271172,1.09653269025677,2.34520029762963,1.45038372655993,No PCV -Netherlands.post.PCV7,36,660,232251,4,1,0,adjusted_type_specific_poisson,0.00295336060740258,0.000362347701530695,0.00824563811583995,0.112358990603774,0.0781814563989282,0.155318386005972,0.000211384916000071,1.20317230766708e-06,0.00166520932006513,1.94921800088571,0.239149483010259,5.44212115645437,0.0546736946602719,0.000160167420584923,0.448214348832013,0.949218000885705,0.0546736946602719,No PCV -Netherlands.post.PCV7,38,660,232251,4,3,0,adjusted_type_specific_poisson,0.00519993464369154,0.00139428668566737,0.0115284178797019,0.112358990603774,0.0781814563989282,0.155318386005972,0.00107630112860654,0.000517329118040196,0.00192400799311281,3.43195686483642,0.920229212540462,7.60875580060328,0.569985939496329,0.125999253106425,1.45568732526521,0.431956864836416,0.569985939496329,No PCV -Netherlands.post.PCV7,4,660,232251,4,1,0,adjusted_type_specific_poisson,0.002200155434528,0.000261569805845126,0.00607090361311057,0.112358990603774,0.0781814563989282,0.155318386005972,0.00249105790199758,0.00143369758150515,0.00400799422771078,1.45210258678848,0.172636071857783,4.00679638465298,0.5551506530496,0.0634455133567051,1.63302180199498,0.452102586788477,0.5551506530496,PCV7 -Netherlands.post.PCV7,42,660,232251,4,1,0,adjusted_type_specific_poisson,0.00298589461812959,0.000358703637987,0.00831941158226603,0.112358990603774,0.0781814563989282,0.155318386005972,0.000106976485278402,1.13850123454097e-06,0.000791514809070834,1.97069044796553,0.23674440107142,5.49081164429558,0.0305323350349735,0.000135850373699959,0.24192559053494,0.970690447965527,0.0305323350349735,No PCV -Netherlands.post.PCV7,6A,660,232251,4,25,0,adjusted_type_specific_poisson,0.0366538257129204,0.0241209686669251,0.0517807765998311,0.112358990603774,0.0781814563989282,0.155318386005972,0.000470534749603847,0.000335293276070173,0.000638312814574088,24.1915249705275,15.9198393201706,34.1753125558885,1.77621200160824,1.01287144822562,2.85539360186589,0.808475029472543,1.77621200160824,PCV13 -Netherlands.post.PCV7,6B,660,232251,4,9,0,adjusted_type_specific_poisson,0.0135105102528491,0.00640439666955339,0.0231374162090948,0.112358990603774,0.0781814563989282,0.155318386005972,0.000770579380902745,0.000565085521465747,0.00101866271810419,8.91693676688044,4.22690180190524,15.2706946980026,1.07072670802602,0.474852400626519,1.96517026880371,0.083063233119562,1.07072670802602,PCV7 -Netherlands.post.PCV7,6C,660,232251,4,14,0,adjusted_type_specific_poisson,0.02233528451074,0.012475020600343,0.0348845518719372,0.112358990603774,0.0781814563989282,0.155318386005972,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,14.7412877770884,8.23351359622637,23.0238042354786,0.235683542369944,0.0817513900041627,0.50803310584431,0.741287777088409,0.235683542369944,No PCV -Netherlands.post.PCV7,7F,660,232251,4,4,13,adjusted_type_specific_poisson,0.0107866238235629,0.00598096846314463,0.0171807232037216,0.112358990603774,0.0781814563989282,0.155318386005972,0.00997721126084835,0.00681051079664878,0.01416409744657,7.11917172355148,3.94743918567545,11.3392773144563,10.8269114463579,6.22192231198733,16.7374672170775,3.11917172355148,2.17308855364211,PCV10 -Netherlands.post.PCV7,8,660,232251,4,5,4,adjusted_type_specific_poisson,0.011001583699433,0.00516202518992229,0.0191041170030956,0.112358990603774,0.0781814563989282,0.155318386005972,0.00244545634969096,0.00123914949735586,0.00432306004960451,7.26104524162579,3.40693662534871,12.6087172220431,2.69674377488785,1.07816836937572,5.25196889697496,2.26104524162579,1.30325622511215,PCV20 -Netherlands.post.PCV7,9N,660,232251,4,2,0,adjusted_type_specific_poisson,0.0041142212439528,0.000842980126462621,0.0100213432282329,0.112358990603774,0.0781814563989282,0.155318386005972,0.00065486417300752,0.000292518419108024,0.00122095961399422,2.71538602100885,0.55636688346533,6.61408653063371,0.274808308585413,0.0455738753504097,0.772076642094857,0.715386021008848,0.274808308585413,PPV23 -Netherlands.post.PCV7,9V,660,232251,4,1,1,adjusted_type_specific_poisson,0.00324922477944277,0.000670657161345259,0.007841258774527,0.112358990603774,0.0781814563989282,0.155318386005972,0.00259101673359874,0.00162148522659737,0.00391316735192488,2.14448835443223,0.442633726487871,5.17523079118782,0.854168854685509,0.169403428324535,2.14672622918768,1.14448835443223,0.145831145314491,PCV7 -Netherlands.pre.PCV,1,321,250924,2,1,4,adjusted_type_specific_poisson,0.00239637903776401,0.000783017210786013,0.0050901558356498,0.224646104503985,0.157087663452603,0.3119543376164,0.0206062908877376,0.0133467842050282,0.0309526551119594,0.769237671122248,0.25134852466231,1.63394002324359,5.24136464548587,1.89683830577443,10.1862332377506,0.230762328877752,1.24136464548587,PCV10 -Netherlands.pre.PCV,10A,321,250924,2,1,1,adjusted_type_specific_poisson,0.00728719152745304,0.00155156008185668,0.0175016877037856,0.224646104503985,0.157087663452603,0.3119543376164,0.000793695374669934,0.000513989148006867,0.00115253233769801,2.33918848031243,0.498050786275994,5.61804175291516,0.637458992162854,0.129764014176186,1.58863875956516,1.33918848031243,0.362541007837146,PCV20 -Netherlands.pre.PCV,11A,321,250924,2,10,0,adjusted_type_specific_poisson,0.0331133231536486,0.0167610940058926,0.0549691452497859,0.224646104503985,0.157087663452603,0.3119543376164,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,10.6293767323212,5.38031117589153,17.6450956251813,0.315032114245914,0.116460410795329,0.652839567807923,0.629376732321205,0.315032114245914,PCV20 -Netherlands.pre.PCV,14,321,250924,2,8,28,adjusted_type_specific_poisson,0.0429733705506993,0.0286435373344504,0.0604161698400629,0.224646104503985,0.157087663452603,0.3119543376164,0.00486577684119951,0.00359593248342883,0.00641271837258626,13.7944519467745,9.19457548435859,19.3935905186602,22.9067334274768,15.720518703882,31.4952966726372,5.79445194677448,5.09326657252316,PCV7 -Netherlands.pre.PCV,15A,321,250924,2,2,0,adjusted_type_specific_poisson,0.00809667153047,0.00160844597727827,0.0197306835389688,0.224646104503985,0.157087663452603,0.3119543376164,0.000447893348168094,0.000276077603700969,0.000677854020290881,2.59903156128087,0.516311158706326,6.33354941600899,0.401448013722538,0.0731389147502357,1.03698607326716,0.59903156128087,0.401448013722538,No PCV -Netherlands.pre.PCV,15B/C,321,250924,2,10,2,adjusted_type_specific_poisson,0.0352423208671361,0.0186960003264341,0.0566038657514179,0.224646104503985,0.157087663452603,0.3119543376164,0.000410284575081173,0.000285934443755961,0.000563977573171364,11.3127849983507,6.00141610478534,18.1698409062051,1.6047734818097,0.772406989643877,2.82345911101018,1.3127849983507,0.395226518190303,PCV20 -Netherlands.pre.PCV,16F,321,250924,2,4,0,adjusted_type_specific_poisson,0.013482171925263,0.00448440817401484,0.0273699106331445,0.224646104503985,0.157087663452603,0.3119543376164,0.000442387133406364,0.000231326668676358,0.000740352472096137,4.32777718800942,1.43949502385876,8.78574131323938,0.656130051314442,0.18309349179215,1.51146398414398,0.327777188009418,0.656130051314442,No PCV -Netherlands.pre.PCV,17F,321,250924,2,1,1,adjusted_type_specific_poisson,0.00817231512986155,0.00170658480636581,0.0197111273921394,0.224646104503985,0.157087663452603,0.3119543376164,0.000400957354522875,0.000201346292292629,0.000689191021815353,2.62331315668556,0.547813722843425,6.32727189287673,0.360459254073082,0.0645361629903635,0.960172981033075,1.62331315668556,0.639540745926918,PPV23 -Netherlands.pre.PCV,18C,321,250924,2,4,6,adjusted_type_specific_poisson,0.0158836778752477,0.00758788418723388,0.0274601742670628,0.224646104503985,0.157087663452603,0.3119543376164,0.00341462550925104,0.0021814214974022,0.00511035484325696,5.09866059795451,2.43571082410207,8.81471593972715,5.87391438087277,2.81751364562112,10.09567012544,1.09866059795451,0.126085619127235,PCV7 -Netherlands.pre.PCV,19A,321,250924,2,9,5,adjusted_type_specific_poisson,0.0280113258322845,0.0155844763337809,0.0443265825743011,0.224646104503985,0.157087663452603,0.3119543376164,0.00193665997116141,0.00151058619668583,0.00243196471893208,8.99163559216331,5.00261690314367,14.2288330063506,5.9952851720909,3.25430481786294,9.62295641959797,0.00836440783668735,0.995285172090898,PCV13 -Netherlands.pre.PCV,19F,321,250924,2,24,4,adjusted_type_specific_poisson,0.0717974751734668,0.0480122913082247,0.0998751146458073,0.224646104503985,0.157087663452603,0.3119543376164,0.000752568056083617,0.000550123319373138,0.00100157805364369,23.0469895306828,15.4119455099401,32.0599118013042,5.98123874866676,3.66719453548149,9.01071319377088,0.953010469317153,1.98123874866676,PCV7 -Netherlands.pre.PCV,21,321,250924,2,2,0,adjusted_type_specific_poisson,0.00860040582363385,0.00180834621187347,0.0207288278832547,0.224646104503985,0.157087663452603,0.3119543376164,0.000234606065585659,0.00010602199615295,0.000423079520489989,2.76073026938647,0.580479134011383,6.65395375052477,0.223122464592182,0.037673127063754,0.621023970671587,0.760730269386467,0.223122464592182,No PCV -Netherlands.pre.PCV,22F,321,250924,2,2,0,adjusted_type_specific_poisson,0.00675351672804087,0.00143018443850658,0.0160821545360953,0.224646104503985,0.157087663452603,0.3119543376164,0.00111291794656347,0.000747288532056908,0.00157611065350571,2.16787886970112,0.459089204760612,5.1623716060866,0.828984152242081,0.170987793278411,2.0351554442048,0.16787886970112,0.828984152242081,PCV15 -Netherlands.pre.PCV,23A,321,250924,2,1,1,adjusted_type_specific_poisson,0.00872027798512875,0.00180081316405863,0.020747593645923,0.224646104503985,0.157087663452603,0.3119543376164,0.00017858253466746,0.000100358645533425,0.000284446850590249,2.79920923322633,0.578061025662819,6.6599775603413,0.173125805802425,0.0311028219449846,0.45796304808118,1.79920923322633,0.826874194197575,No PCV -Netherlands.pre.PCV,23B,321,250924,2,12,0,adjusted_type_specific_poisson,0.0366320376856334,0.0196625891369435,0.0585257935762805,0.224646104503985,0.157087663452603,0.3119543376164,0.000290469676688038,0.000174295346379655,0.000444118199022155,11.7588840970883,6.31169111295887,18.786779737986,1.1808826548732,0.521276010702372,2.1957600570933,0.241115902911691,1.1808826548732,No PCV -Netherlands.pre.PCV,23F,321,250924,2,28,4,adjusted_type_specific_poisson,0.0813188120619419,0.055956605686101,0.111357451908951,0.224646104503985,0.157087663452603,0.3119543376164,0.00077564137009531,0.000556479798610777,0.00105106918760042,26.1033386718833,17.9620704252384,35.7457420627733,6.97124446338615,4.40121543197226,10.3020904996,1.89666132811666,2.97124446338615,PCV7 -Netherlands.pre.PCV,24F,321,250924,2,1,0,adjusted_type_specific_poisson,0.00312145828880929,0.000377558923360918,0.00877013201661095,0.224646104503985,0.157087663452603,0.3119543376164,0.00296592942741409,0.00168198604203905,0.00494246465975427,1.00198811070778,0.121196414398855,2.81521237733211,0.988451135884147,0.120290321327425,2.78626143826248,0.00198811070778371,0.988451135884147,No PCV -Netherlands.pre.PCV,3,321,250924,2,3,1,adjusted_type_specific_poisson,0.00897083241368606,0.00286352912467674,0.0184522312233262,0.224646104503985,0.157087663452603,0.3119543376164,0.00214630789735218,0.00150111695338643,0.00296037810122135,2.87963720479323,0.919192849021235,5.9231662226877,2.11258266434896,0.674901213750021,4.43798186391644,0.120362795206774,1.11258266434896,PCV13 -Netherlands.pre.PCV,33F,321,250924,2,6,1,adjusted_type_specific_poisson,0.0165815199488557,0.00702746725327455,0.030123478292586,0.224646104503985,0.157087663452603,0.3119543376164,0.00147980242560294,0.000904545029211608,0.00226255226693128,5.32266790358267,2.25581698830113,9.66963653192012,2.68265668778129,1.06252681601749,5.16576893068077,0.67733209641733,1.68265668778129,PCV15 -Netherlands.pre.PCV,35B,321,250924,2,2,0,adjusted_type_specific_poisson,0.00890399086766628,0.00181666996269875,0.0214933091784956,0.224646104503985,0.157087663452603,0.3119543376164,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,2.85818106852088,0.5831510580263,6.89935224629708,0.142516778843284,0.0243537900096004,0.393211559933821,0.858181068520876,0.142516778843284,No PCV -Netherlands.pre.PCV,38,321,250924,2,1,0,adjusted_type_specific_poisson,0.00457937022497422,0.000552661908370585,0.0128207434475483,0.224646104503985,0.157087663452603,0.3119543376164,0.00107630112860654,0.000517329118040196,0.00192400799311281,1.46997784221672,0.177404472586958,4.11545864666301,0.533736884289889,0.0581729265774794,1.60755557171242,0.469977842216723,0.533736884289889,No PCV -Netherlands.pre.PCV,4,321,250924,2,1,2,adjusted_type_specific_poisson,0.00677515860789039,0.00176336782323678,0.0153371033427278,0.224646104503985,0.157087663452603,0.3119543376164,0.00249105790199758,0.00143369758150515,0.00400799422771078,2.17482591313282,0.566041071259008,4.92321017301562,1.8188245443787,0.463561289973527,4.18454458067906,1.17482591313282,0.181175455621303,PCV7 -Netherlands.pre.PCV,6A,321,250924,2,25,5,adjusted_type_specific_poisson,0.0823229360559387,0.0561796186292125,0.112816828165906,0.224646104503985,0.157087663452603,0.3119543376164,0.000470534749603847,0.000335293276070173,0.000638312814574088,26.4256624739563,18.0336575799772,36.2142018412557,4.2900475154058,2.61097479173871,6.49582873187762,1.42566247395633,0.709952484594201,PCV13 -Netherlands.pre.PCV,6B,321,250924,2,43,16,adjusted_type_specific_poisson,0.145604116845028,0.112310117150275,0.183004702017081,0.224646104503985,0.157087663452603,0.3119543376164,0.000770579380902745,0.000565085521465747,0.00101866271810419,46.7389215072539,36.0515476052381,58.7445093474829,12.4102719304856,8.61706420398481,17.1330577066714,3.73892150725391,3.58972806951443,PCV7 -Netherlands.pre.PCV,7F,321,250924,2,0,8,adjusted_type_specific_poisson,0.00645179093502232,0.00267008095616781,0.012262223936306,0.224646104503985,0.157087663452603,0.3119543376164,0.00997721126084835,0.00681051079664878,0.01416409744657,2.07102489014216,0.857095986929867,3.93617388355422,6.93154973848553,3.09528517144059,12.2626715962593,2.07102489014216,1.06845026151447,PCV10 -Netherlands.pre.PCV,8,321,250924,2,0,2,adjusted_type_specific_poisson,0.0051356387305759,0.00105390301632431,0.0126054280364165,0.224646104503985,0.157087663452603,0.3119543376164,0.00244545634969096,0.00123914949735586,0.00432306004960451,1.64854003251486,0.338302868240103,4.04634239968971,1.33602273531963,0.267612120254717,3.34807645135423,1.64854003251486,0.66397726468037,PCV20 -Netherlands.pre.PCV,9N,321,250924,2,1,1,adjusted_type_specific_poisson,0.00762015255910347,0.00159189071175897,0.0182342882352827,0.224646104503985,0.157087663452603,0.3119543376164,0.00065486417300752,0.000292518419108024,0.00122095961399422,2.44606897147221,0.51099691847463,5.85320652352576,0.543472820467572,0.0967656230581483,1.46689287096562,1.44606897147221,0.456527179532428,PPV23 -Netherlands.pre.PCV,9V,321,250924,2,6,8,adjusted_type_specific_poisson,0.02478858256113,0.0133461391443383,0.0402617169088507,0.224646104503985,0.157087663452603,0.3119543376164,0.00259101673359874,0.00162148522659737,0.00391316735192488,7.95713500212273,4.28411066533259,12.9240111277411,6.96830395004912,3.66931616607429,11.4814169777482,1.95713500212273,1.03169604995088,PCV7 -Portugal.pre.PCV,1,1170,2071223,2,1,15,adjusted_type_specific_poisson,0.00512274373241931,0.00271910005677012,0.00845344412731875,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.0206062908877376,0.0133467842050282,0.0309526551119594,5.99361016693059,3.18134706642104,9.89052962896293,10.996312105292,6.2710174903072,17.1851511094559,4.99361016693059,4.00368789470801,PCV10 -Portugal.pre.PCV,10A,1170,2071223,2,19,2,adjusted_type_specific_poisson,0.0174485714227439,0.0109709622554735,0.0253424620180409,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000793695374669934,0.000513989148006867,0.00115253233769801,20.4148285646103,12.8360258389039,29.6506805611079,1.48835916716696,0.785887347849851,2.48062384002952,1.41482856461033,0.511640832833035,PCV20 -Portugal.pre.PCV,11A,1170,2071223,2,42,0,adjusted_type_specific_poisson,0.0364315061644763,0.0265480459215778,0.0478941409298365,0.0263050665310201,0.0187370666138758,0.0358307383434996,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,42.6248622124372,31.061213728246,56.0361448879087,0.336107802485043,0.15025000449269,0.616586208833991,0.624862212437215,0.336107802485043,PCV20 -Portugal.pre.PCV,14,1170,2071223,2,52,12,adjusted_type_specific_poisson,0.0386315225323558,0.0293843048649497,0.0491639619205629,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00486577684119951,0.00359593248342883,0.00641271837258626,45.1988813628563,34.3796366919911,57.5218354470586,20.0693433019872,14.4175336751623,26.8605826182886,6.80111863714368,8.06934330198721,PCV7 -Portugal.pre.PCV,15A,1170,2071223,2,4,0,adjusted_type_specific_poisson,0.00408540048281942,0.00133620652196593,0.00826055709523704,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000447893348168094,0.000276077603700969,0.000677854020290881,4.77991856489872,1.56336163070014,9.66485180142734,0.197279445391708,0.0567494194064329,0.446218142574489,0.77991856489872,0.197279445391708,No PCV -Portugal.pre.PCV,15B/C,1170,2071223,2,33,1,adjusted_type_specific_poisson,0.0287791483805476,0.0201328857763131,0.0388350537100681,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000410284575081173,0.000285934443755961,0.000563977573171364,33.6716036052407,23.5554763582864,45.4370128407797,1.27075273788796,0.755131365899627,1.99145677497261,0.671603605240712,0.27075273788796,PCV20 -Portugal.pre.PCV,16F,1170,2071223,2,36,0,adjusted_type_specific_poisson,0.0303582699285892,0.0215147401781559,0.0405411880853822,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000442387133406364,0.000231326668676358,0.000740352472096137,35.5191758164494,25.1722460084424,47.4331900598972,1.44296141477019,0.689061516946293,2.59126029126716,0.480824183550588,1.44296141477019,No PCV -Portugal.pre.PCV,18A,1170,2071223,2,12,0,adjusted_type_specific_poisson,0.010790988565416,0.00583291493906131,0.0172086721992813,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000283343585215039,2.68111527639592e-05,0.000946066820544266,12.6254566215367,6.82451047870173,20.1341464731592,0.322491313861049,0.0290117723304523,1.09790158952912,0.62545662153669,0.322491313861049,No PCV -Portugal.pre.PCV,18C,1170,2071223,2,13,6,adjusted_type_specific_poisson,0.0130136386219937,0.00787781848716337,0.019416163955019,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00341462550925104,0.0021814214974022,0.00511035484325696,15.2259571877326,9.21704762998114,22.7169118273723,4.72328445318633,2.60197300322573,7.67579718597318,2.22595718773263,1.27671554681367,PCV7 -Portugal.pre.PCV,19A,1170,2071223,2,45,11,adjusted_type_specific_poisson,0.0412266399849209,0.0312746069283236,0.0523582164908356,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00193665997116141,0.00151058619668583,0.00243196471893208,48.2351687823575,36.5912901061387,61.2591132942777,8.58371345049144,5.87784839463162,11.8980751225902,3.23516878235746,2.41628654950856,PCV13 -Portugal.pre.PCV,19F,1170,2071223,2,93,1,adjusted_type_specific_poisson,0.0761124235252768,0.0618683804832987,0.0916946175011596,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000752568056083617,0.000550123319373138,0.00100157805364369,89.0515355245738,72.3860051654595,107.282702476357,6.15296409933548,4.24353229678464,8.55898617080195,3.94846447542616,5.15296409933548,PCV7 -Portugal.pre.PCV,20,1170,2071223,2,0,1,adjusted_type_specific_poisson,0.00157172081629046,0.000185431746315235,0.00439760461313737,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000957797173992484,0.000238388518107766,0.00247568343665466,1.83891335505984,0.216955143188825,5.14519739737073,0.158263001489942,0.0120616160733218,0.578155325603568,1.83891335505984,0.841736998510058,PPV23 -Portugal.pre.PCV,21,1170,2071223,2,6,0,adjusted_type_specific_poisson,0.0058480918620569,0.0023316434726375,0.0108973720039408,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000234606065585659,0.00010602199615295,0.000423079520489989,6.84226747860658,2.72802286298587,12.7499252446107,0.147709070979892,0.0433045244920549,0.34689276133867,0.842267478606575,0.147709070979892,No PCV -Portugal.pre.PCV,22F,1170,2071223,2,8,0,adjusted_type_specific_poisson,0.00695673977528771,0.00319317329519672,0.0120534039830474,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00111291794656347,0.000747288532056908,0.00157611065350571,8.13938553708662,3.73601275538017,14.1024826601654,0.833048843080281,0.344647703433032,1.58490659488638,0.139385537086625,0.833048843080281,PCV15 -Portugal.pre.PCV,23A,1170,2071223,2,11,0,adjusted_type_specific_poisson,0.0100679403231367,0.005232430303942,0.016440630876292,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00017858253466746,0.000100358645533425,0.000284446850590249,11.7794901780699,6.12194345561214,19.2355381252617,0.193554203692722,0.0791190421362182,0.379997157024992,0.779490178069896,0.193554203692722,No PCV -Portugal.pre.PCV,23B,1170,2071223,2,11,1,adjusted_type_specific_poisson,0.010798961561671,0.00574620957439419,0.017366350027181,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000290469676688038,0.000174295346379655,0.000444118199022155,12.634785027155,6.7230652020412,20.3186295318018,0.338207825084301,0.145739252513323,0.641705876072296,1.63478502715503,0.661792174915699,No PCV -Portugal.pre.PCV,23F,1170,2071223,2,70,13,adjusted_type_specific_poisson,0.0664847199627814,0.0534127010684367,0.0808353032633333,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00077564137009531,0.000556479798610777,0.00105106918760042,77.7871223564542,62.492860250071,94.5773048181,5.53813641796017,3.74767118100118,7.8346646193814,7.78712235645418,7.46186358203983,PCV7 -Portugal.pre.PCV,24F,1170,2071223,2,3,0,adjusted_type_specific_poisson,0.00269059789232516,0.000715360912518666,0.00597974536711982,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00296592942741409,0.00168198604203905,0.00494246465975427,3.14799953402043,0.836972267646839,6.99630207953019,0.845372465229999,0.206637598654153,2.03193671714128,0.147999534020435,0.845372465229999,No PCV -Portugal.pre.PCV,3,1170,2071223,2,28,5,adjusted_type_specific_poisson,0.0242701589966643,0.016758683022084,0.033151825759959,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00214630789735218,0.00150111695338643,0.00296037810122135,28.3960860260972,19.6076591358383,38.787636139152,5.58542673056894,3.40583338891158,8.50889549102136,0.396086026097205,0.585426730568943,PCV13 -Portugal.pre.PCV,31,1170,2071223,2,7,1,adjusted_type_specific_poisson,0.00731062334545794,0.003346972991862,0.0128458794525056,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000529235275657269,0.000187950733188048,0.00110145716265855,8.55342931418579,3.91595840047854,15.0296789594316,0.413449264445494,0.114432737490085,0.99520443400436,1.55342931418579,0.586550735554506,No PCV -Portugal.pre.PCV,33F,1170,2071223,2,4,1,adjusted_type_specific_poisson,0.00450311251539486,0.00165229109054132,0.00874372794050707,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00147980242560294,0.000904545029211608,0.00226255226693128,5.26864164301198,1.93318057593334,10.2301616903933,0.714782073055793,0.233191612953568,1.53198957127892,1.26864164301198,0.285217926944207,PCV15 -Portugal.pre.PCV,34,1170,2071223,2,18,0,adjusted_type_specific_poisson,0.0160605741024913,0.00976654027767113,0.0239933159068299,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,18.7908716999149,11.4268521248752,28.072179610991,0.204111122717972,0.0369525343557478,0.5533175198416,0.79087169991487,0.204111122717972,No PCV -Portugal.pre.PCV,35F,1170,2071223,2,35,1,adjusted_type_specific_poisson,0.031051852646699,0.022114513458256,0.0416145666815618,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,36.3306675966378,25.8739807461596,48.6890430174274,0.607533405947663,0.26185208777887,1.14319920193691,1.33066759663782,0.392466594052337,No PCV -Portugal.pre.PCV,37,1170,2071223,2,9,0,adjusted_type_specific_poisson,0.00844045181643425,0.00404446698831849,0.0144059198127656,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000155201681937787,5.20169758717572e-06,0.000602123592537372,9.87532862522807,4.73202637633263,16.8549261809358,0.138634175969986,0.00426408124694529,0.560257823492229,0.875328625228072,0.138634175969986,No PCV -Portugal.pre.PCV,4,1170,2071223,2,4,0,adjusted_type_specific_poisson,0.00348799015311609,0.00113361874652636,0.00715087047256253,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00249105790199758,0.00143369758150515,0.00400799422771078,4.08094847914583,1.32633393343584,8.36651845289816,0.924359359323356,0.266648227176713,2.0814714835316,0.0809484791458255,0.924359359323356,PCV7 -Portugal.pre.PCV,5,1170,2071223,2,0,1,adjusted_type_specific_poisson,0.000967615290546839,0.000113445757146122,0.00278180063994819,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00898185496955944,0.00375244500011871,0.0188069207217874,1.1321098899398,0.132731535860963,3.25470674873938,0.865847917422584,0.0963188652260455,2.53173217220193,1.1321098899398,0.134152082577416,PCV10 -Portugal.pre.PCV,6A,1170,2071223,2,64,3,adjusted_type_specific_poisson,0.0555634354413988,0.0433575242163887,0.0692678126819816,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000470534749603847,0.000335293276070173,0.000638312814574088,65.0092194664366,50.7283033331748,81.0433408379185,2.8091653998376,1.85873227472503,4.05756359549014,1.00921946643662,0.190834600162398,PCV13 -Portugal.pre.PCV,6B,1170,2071223,2,69,5,adjusted_type_specific_poisson,0.0597625253226851,0.0472097625338282,0.0735622340204839,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000770579380902745,0.000565085521465747,0.00101866271810419,69.9221546275416,55.2354221645789,86.0678138039662,4.94630813999445,3.37632389358461,6.93217025619545,0.922154627541588,0.0536918600055492,PCV7 -Portugal.pre.PCV,6C,1170,2071223,2,14,0,adjusted_type_specific_poisson,0.0126793972977534,0.00712420674850536,0.0197930792854808,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,14.8348948383714,8.33532189575127,23.1579027640125,0.139675659612131,0.0489608404615093,0.301776526269114,0.834894838371433,0.139675659612131,No PCV -Portugal.pre.PCV,7F,1170,2071223,2,3,4,adjusted_type_specific_poisson,0.00358784268973501,0.00152581237933542,0.00657700831558572,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00997721126084835,0.00681051079664878,0.01416409744657,4.19777594698996,1.78520048382244,7.69509972923529,3.78749150992831,1.6083890566489,7.02961493463729,1.19777594698996,0.212508490071693,PCV10 -Portugal.pre.PCV,8,1170,2071223,2,1,1,adjusted_type_specific_poisson,0.00209916736604682,0.000432832935852628,0.00506726611445745,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00244545634969096,0.00123914949735586,0.00432306004960451,2.45602581827478,0.506414534947575,5.92870135391521,0.54213411946186,0.0993782455640476,1.43819675883085,1.45602581827478,0.45786588053814,PCV20 -Portugal.pre.PCV,9L,1170,2071223,2,0,1,adjusted_type_specific_poisson,0.00127163832421715,0.000119439355817032,0.00383404170443982,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00651481161652821,0.000202150097442497,0.0350412259425872,1.48781683933407,0.139744046305927,4.48582879419459,0.500539765280522,0.0153103338451445,2.18732040700879,1.48781683933407,0.499460234719478,No PCV -Portugal.pre.PCV,9N,1170,2071223,2,1,1,adjusted_type_specific_poisson,0.00241203069430168,0.000483507425628253,0.00584422618296656,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00065486417300752,0.000292518419108024,0.00122095961399422,2.82207591233296,0.565703687985057,6.83774463407087,0.168036322545959,0.0279358246507,0.467396848461995,1.82207591233296,0.831963677454041,PPV23 -Portugal.pre.PCV,9V,1170,2071223,2,14,2,adjusted_type_specific_poisson,0.011749842218653,0.00680299915199313,0.0180598017714051,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.00259101673359874,0.00162148522659737,0.00391316735192488,13.747315395824,7.95950900783196,21.129968072544,3.23792140162921,1.67474062331593,5.46376150105168,0.252684604176004,1.23792140162921,PCV7 -Portugal.pre.PCV,19C,1170,2071223,2,0,1,adjusted_type_specific_poisson,0.000853034139496718,2.61183191548939e-05,0.00313658585543369,0.0263050665310201,0.0187370666138758,0.0358307383434996,0.057311879682744,0.000265003148392281,0.36603675528849,0.998049943211161,0.0305584334112259,3.66980545085742,1.00636762097771,0.0248713697969519,3.74100478181765,0.998049943211161,0.00636762097770838,No PCV -E.W.pre.PCV,10A,3752,3091000,1,1,0,adjusted_type_specific_poisson,0.000365745344692259,4.28987724724373e-05,0.00103354739028782,0.725836589039311,0.551118154868677,0.939573612607357,0.000793695374669934,0.000513989148006867,0.00115253233769801,1.37227653328536,0.160956194316585,3.87786980835989,0.635137353191835,0.0724617174573291,1.80364654506333,0.372276533285355,0.635137353191835,PCV20 -E.W.pre.PCV,11A,3752,3091000,1,25,2,adjusted_type_specific_poisson,0.00710819560464855,0.00468417241166083,0.00998731359345949,0.725836589039311,0.551118154868677,0.939573612607357,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,26.6699499086413,17.5750148885514,37.47240060266,1.34506152227438,0.609071023093927,2.45227288687382,1.66994990864135,0.654938477725623,PCV20 -E.W.pre.PCV,14,3752,3091000,1,58,125,adjusted_type_specific_poisson,0.0127641268563476,0.0102504918586867,0.0155874278757564,0.725836589039311,0.551118154868677,0.939573612607357,0.00486577684119951,0.00359593248342883,0.00641271837258626,47.8910039650162,38.4598454537926,58.4840293898382,136.216169990125,116.025088363498,158.307917070139,10.1089960349838,11.2161699901245,PCV7 -E.W.pre.PCV,15B/C,3752,3091000,1,15,8,adjusted_type_specific_poisson,0.00514471409401698,0.00329062825206301,0.00740406556792315,0.725836589039311,0.551118154868677,0.939573612607357,0.000410284575081173,0.000285934443755961,0.000563977573171364,19.3029672807517,12.3464372017404,27.7800540108476,4.6622677896365,2.73674401391148,7.20193117468306,4.30296728075172,3.3377322103635,PCV20 -E.W.pre.PCV,16F,3752,3091000,1,2,2,adjusted_type_specific_poisson,0.00106030241700061,0.000339969844538366,0.00218284745533602,0.725836589039311,0.551118154868677,0.939573612607357,0.000442387133406364,0.000231326668676358,0.000740352472096137,3.97825466858631,1.27556685670795,8.19004365242074,1.02227364762556,0.296327110837343,2.31105148124686,1.97825466858631,0.977726352374437,No PCV -E.W.pre.PCV,17F,3752,3091000,1,0,1,adjusted_type_specific_poisson,0.00043124811888265,5.05788884762309e-05,0.00118760788227486,0.725836589039311,0.551118154868677,0.939573612607357,0.000400957354522875,0.000201346292292629,0.000689191021815353,1.6180429420477,0.189771989562818,4.45590477429526,0.377156722038254,0.0421307753009296,1.11726850952143,1.6180429420477,0.622843277961746,PPV23 -E.W.pre.PCV,18B,3752,3091000,1,2,1,adjusted_type_specific_poisson,0.000590237724938969,0.00012498182121424,0.00147666700569686,0.725836589039311,0.551118154868677,0.939573612607357,0.00173622469177418,0.00030591934704866,0.00552384967796135,2.21457194397101,0.468931793195828,5.54045460537461,1.7870814721781,0.330801131610717,4.64941025978593,0.214571943971013,0.787081472178099,No PCV -E.W.pre.PCV,18C,3752,3091000,1,12,41,adjusted_type_specific_poisson,0.00485388880494482,0.00326454184048125,0.00678080508898657,0.725836589039311,0.551118154868677,0.939573612607357,0.00341462550925104,0.0021814214974022,0.00511035484325696,18.211790796153,12.2485609854856,25.4415806938776,35.7778848346061,26.1326884476144,47.1604963935827,6.21179079615296,5.22211516539394,PCV7 -E.W.pre.PCV,19A,3752,3091000,1,18,20,adjusted_type_specific_poisson,0.00486345496452177,0.00336846295005028,0.0066360602551271,0.725836589039311,0.551118154868677,0.939573612607357,0.00193665997116141,0.00151058619668583,0.00243196471893208,18.2476830268857,12.6384729885886,24.8984980772369,20.7745691432767,14.4992125432468,28.2130947421544,0.247683026885664,0.77456914327669,PCV13 -E.W.pre.PCV,19F,3752,3091000,1,92,52,adjusted_type_specific_poisson,0.0267708733044619,0.0222526602786351,0.0316942898700001,0.725836589039311,0.551118154868677,0.939573612607357,0.000752568056083617,0.000550123319373138,0.00100157805364369,100.444316638341,83.491981365439,118.91697559224,44.3737283043408,35.1428900656765,54.9314749096559,8.44431663834111,7.62627169565917,PCV7 -E.W.pre.PCV,20,3752,3091000,1,0,1,adjusted_type_specific_poisson,0.00035334462508633,3.88807478580785e-05,0.00103144293895364,0.725836589039311,0.551118154868677,0.939573612607357,0.000957797173992484,0.000238388518107766,0.00247568343665466,1.32574903332391,0.145880565963511,3.86997390695407,0.668453511836764,0.0638004799314497,2.13645048629838,1.32574903332391,0.331546488163236,PPV23 -E.W.pre.PCV,21,3752,3091000,1,4,0,adjusted_type_specific_poisson,0.00116881255152053,0.000378796684630269,0.00241538309152081,0.725836589039311,0.551118154868677,0.939573612607357,0.000234606065585659,0.00010602199615295,0.000423079520489989,4.38538469330502,1.42124516073277,9.0625173593861,0.601872500985206,0.157484475861427,1.44546160026219,0.385384693305017,0.601872500985206,No PCV -E.W.pre.PCV,22F,3752,3091000,1,11,9,adjusted_type_specific_poisson,0.00338513499932633,0.00203229183823229,0.0050916464891025,0.725836589039311,0.551118154868677,0.939573612607357,0.00111291794656347,0.000747288532056908,0.00157611065350571,12.7010265174724,7.62515897704754,19.1038576271126,8.25980535923853,4.77125287691484,12.8437023570936,1.7010265174724,0.740194640761469,PCV15 -E.W.pre.PCV,23A,3752,3091000,1,9,2,adjusted_type_specific_poisson,0.00289000859801967,0.0014948462483823,0.00472831124625876,0.725836589039311,0.551118154868677,0.939573612607357,0.00017858253466746,0.000100358645533425,0.000284446850590249,10.8433122597698,5.60866312393039,17.7406237959629,1.1386293860909,0.49175989393497,2.14891676645499,1.84331225976982,0.861370613909105,No PCV -E.W.pre.PCV,23F,3752,3091000,1,88,43,adjusted_type_specific_poisson,0.0241630825382238,0.0199949720708567,0.0288518544388872,0.725836589039311,0.551118154868677,0.939573612607357,0.00077564137009531,0.000556479798610777,0.00105106918760042,90.6598856834158,75.0211352098544,108.252157854705,41.2374364450133,32.182602671922,51.4291522689974,2.65988568341579,1.76256355498673,PCV7 -E.W.pre.PCV,27,3752,3091000,1,1,1,adjusted_type_specific_poisson,0.000203948328928363,2.77137572932489e-05,0.000606355825848358,0.725836589039311,0.551118154868677,0.939573612607357,0.00667616951433804,0.00152734556090641,0.0197265487315555,0.765214130139216,0.10398201736427,2.27504705858304,2.23709075713558,0.438227428656691,5.53313809406264,0.234785869860784,1.23709075713558,No PCV -E.W.pre.PCV,3,3752,3091000,1,4,6,adjusted_type_specific_poisson,0.00130228770043038,0.000643568778135759,0.00221392569237113,0.725836589039311,0.551118154868677,0.939573612607357,0.00214630789735218,0.00150111695338643,0.00296037810122135,4.88618345201478,2.41467005556537,8.30664919777647,6.11267020799087,3.05413484780389,10.3674897526533,0.886183452014778,0.112670207990869,PCV13 -E.W.pre.PCV,31,3752,3091000,1,1,0,adjusted_type_specific_poisson,0.000409327504011888,4.99748185541892e-05,0.00114756697480654,0.725836589039311,0.551118154868677,0.939573612607357,0.000529235275657269,0.000187950733188048,0.00110145716265855,1.53579679505261,0.187505519215318,4.30567128947415,0.459938374090267,0.0466966813489947,1.42931828248673,0.535796795052605,0.459938374090267,No PCV -E.W.pre.PCV,35B,3752,3091000,1,4,1,adjusted_type_specific_poisson,0.0014764426856882,0.000539966942931982,0.00285997814720197,0.725836589039311,0.551118154868677,0.939573612607357,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,5.53961295670214,2.0259559698808,10.7306380083018,0.470273051068227,0.135737579928313,1.07902255713581,1.53961295670214,0.529726948931773,No PCV -E.W.pre.PCV,35F,3752,3091000,1,15,1,adjusted_type_specific_poisson,0.00409755207321534,0.00236141581834587,0.00629523858937949,0.725836589039311,0.551118154868677,0.939573612607357,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,15.374015378704,8.86003215043369,23.6197351873518,1.63647299670044,0.675534840709869,3.14033789339618,0.374015378703968,0.636472996700437,No PCV -E.W.pre.PCV,38,3752,3091000,1,1,3,adjusted_type_specific_poisson,0.000827869915935494,0.000259211030336683,0.00174977196783571,0.725836589039311,0.551118154868677,0.939573612607357,0.00107630112860654,0.000517329118040196,0.00192400799311281,3.10616792458997,0.972559785823233,6.5651444233196,1.90135953819407,0.554742798992984,4.24622534535747,2.10616792458997,1.09864046180593,No PCV -E.W.pre.PCV,4,3752,3091000,1,0,10,adjusted_type_specific_poisson,0.00121004724403107,0.00056887002607277,0.0021192744317496,0.725836589039311,0.551118154868677,0.939573612607357,0.00249105790199758,0.00143369758150515,0.00400799422771078,4.54009725960459,2.13440033782503,7.9515176679245,6.44139902769572,3.11316671197722,11.0144113863363,4.54009725960459,3.55860097230428,PCV7 -E.W.pre.PCV,6A,3752,3091000,1,82,16,adjusted_type_specific_poisson,0.0206867236515083,0.0167191670915951,0.0250802941085064,0.725836589039311,0.551118154868677,0.939573612607357,0.000470534749603847,0.000335293276070173,0.000638312814574088,77.616587140459,62.7303149276647,94.1012634951159,21.4498100740816,15.9868651345716,27.9900731612423,4.38341285954097,5.44981007408162,PCV13 -E.W.pre.PCV,6B,3752,3091000,1,186,64,adjusted_type_specific_poisson,0.0461965141855577,0.0400853756148519,0.052710273420705,0.725836589039311,0.551118154868677,0.939573612607357,0.000770579380902745,0.000565085521465747,0.00101866271810419,173.329321224213,150.400329306924,197.768945874485,78.3943226960238,64.9312970021393,93.3556639713186,12.6706787757875,14.3943226960238,PCV7 -E.W.pre.PCV,7F,3752,3091000,1,2,10,adjusted_type_specific_poisson,0.000515285645086928,0.000254330829949957,0.000899725538161986,0.725836589039311,0.551118154868677,0.939573612607357,0.00997721126084835,0.00681051079664878,0.01416409744657,1.93335174036615,0.954249273972237,3.37577021918377,11.094167941629,5.94818174100012,17.965760317578,0.0666482596338454,1.094167941629,PCV10 -E.W.pre.PCV,8,3752,3091000,1,0,8,adjusted_type_specific_poisson,0.00101201617673109,0.000420873257609553,0.00192094259889286,0.725836589039311,0.551118154868677,0.939573612607357,0.00244545634969096,0.00123914949735586,0.00432306004960451,3.79708469509506,1.57911646255104,7.20737663104602,5.19231544156176,2.2516437635122,9.5123470248364,3.79708469509506,2.80768455843824,PCV20 -E.W.pre.PCV,9N,3752,3091000,1,4,6,adjusted_type_specific_poisson,0.00213509156249442,0.00102550548940731,0.00367508099181121,0.725836589039311,0.551118154868677,0.939573612607357,0.00065486417300752,0.000292518419108024,0.00122095961399422,8.01086354247905,3.84769659625623,13.7889038812756,2.99018795717882,1.19533412224886,5.7756314137163,4.01086354247905,3.00981204282118,PPV23 -E.W.pre.PCV,9V,3752,3091000,1,11,28,adjusted_type_specific_poisson,0.00428816722743817,0.00279986703882285,0.00613838692838367,0.725836589039311,0.551118154868677,0.939573612607357,0.00259101673359874,0.00162148522659737,0.00391316735192488,16.089203437348,10.5051011296633,23.0312277552955,23.9802063430566,16.4085618764096,33.2280296999858,5.08920343734802,4.01979365694341,PCV7 -France.post.PCV13,10A,1212,842076,2,11,14,adjusted_type_specific_poisson,0.0106982727041984,0.00662621176085126,0.0158447829917646,0.942700102269306,0.674784989520932,1.27891869309046,0.000793695374669934,0.000513989148006867,0.00115253233769801,12.9663065174885,8.03096865415173,19.2038769860186,13.0321292572475,8.05367029911543,19.3552814505661,1.96630651748849,0.967870742752515,PCV20 -France.post.PCV13,10B,1212,842076,2,1,0,adjusted_type_specific_poisson,0.000972035026466153,9.84554085560556e-05,0.00300287860226916,0.942700102269306,0.674784989520932,1.27891869309046,0.000696632980137251,9.61989918783685e-05,0.00234483425439832,1.17810645207698,0.119327955169939,3.63948886595022,0.819604935768115,0.0675206964347387,2.70231836564363,0.178106452076977,0.819604935768115,No PCV -France.post.PCV13,11A,1212,842076,2,13,2,adjusted_type_specific_poisson,0.0118655010304845,0.00681040468963626,0.0182795500792252,0.942700102269306,0.674784989520932,1.27891869309046,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,14.3809872489472,8.25421048383915,22.154814696021,1.5795365033385,0.658573397836994,3.01949583905737,1.38098724894717,0.420463496661502,PCV20 -France.post.PCV13,11B,1212,842076,2,0,1,adjusted_type_specific_poisson,0.000830829074890426,2.00203475325019e-05,0.0030960815779975,0.942700102269306,0.674784989520932,1.27891869309046,0.00631186036248223,1.9312378434922e-05,0.0305470723877019,1.0069648387672,0.0242646612093924,3.75245087253297,1.00202470580227,0.0245585358176546,3.73064450012217,1.0069648387672,0.00202470580226777,No PCV -France.post.PCV13,11F,1212,842076,2,1,0,adjusted_type_specific_poisson,0.00150205976675674,0.000155777692103902,0.00431790476120251,0.942700102269306,0.674784989520932,1.27891869309046,0.000135150214584105,1.13826973717218e-06,0.000990025463844677,1.82049643730917,0.188802562829929,5.23330057057744,0.179201939427201,0.00109084995391308,1.26823109915821,0.820496437309175,0.179201939427201,No PCV -France.post.PCV13,12F,1212,842076,2,0,16,adjusted_type_specific_poisson,0.00138371903864344,0.000615239926730595,0.00263463795064354,0.942700102269306,0.674784989520932,1.27891869309046,0.00763701563010158,0.00413184393687895,0.0128667210227945,1.67706747483584,0.745670791197481,3.19318119617998,15.2741918773343,8.85329993622353,23.4438206055064,1.67706747483584,0.725808122665711,PCV20 -France.post.PCV13,14,1212,842076,2,2,2,adjusted_type_specific_poisson,0.000575707944631366,0.000179564948249374,0.00123715901340618,0.942700102269306,0.674784989520932,1.27891869309046,0.00486577684119951,0.00359593248342883,0.00641271837258626,0.697758028893215,0.217632717278241,1.49943672424829,4.29494511625946,1.40720863002098,8.83889390618677,1.30224197110678,2.29494511625946,PCV7 -France.post.PCV13,15A,1212,842076,2,14,13,adjusted_type_specific_poisson,0.0146787893777844,0.00944916971811981,0.0212246253405861,0.942700102269306,0.674784989520932,1.27891869309046,0.000447893348168094,0.000276077603700969,0.000677854020290881,17.7906927258747,11.4523936983612,25.7242459127904,10.1121007920995,6.0120949093963,15.4241931613527,3.79069272587469,2.88789920790051,No PCV -France.post.PCV13,15B/C,1212,842076,2,22,15,adjusted_type_specific_poisson,0.0205151401009623,0.0142176087246634,0.0280245443476357,0.942700102269306,0.674784989520932,1.27891869309046,0.000410284575081173,0.000285934443755961,0.000563977573171364,24.8643498023663,17.2317417742921,33.9657477493345,13.060408755399,8.52718193420698,18.7820499762595,2.86434980236626,1.93959124460103,PCV20 -France.post.PCV13,15F,1212,842076,2,0,2,adjusted_type_specific_poisson,0.00195140825161676,0.000378711540352196,0.00486577859591245,0.942700102269306,0.674784989520932,1.27891869309046,0.000241837303648991,2.36364376734738e-05,0.000792155722410316,2.36510680095952,0.458998386906861,5.89732365824588,0.642509198173119,0.0481306823876859,2.21278777650237,2.36510680095952,1.35749080182688,No PCV -France.post.PCV13,16F,1212,842076,2,3,1,adjusted_type_specific_poisson,0.00264930839849019,0.000840537495447731,0.00555541662463511,0.942700102269306,0.674784989520932,1.27891869309046,0.000442387133406364,0.000231326668676358,0.000740352472096137,3.2109617789701,1.01873144448265,6.73316494905775,1.77811087395273,0.541595448352774,3.86900305900798,0.210961778970105,0.778110873952728,No PCV -France.post.PCV13,17F,1212,842076,2,8,3,adjusted_type_specific_poisson,0.00658925266881563,0.00328828747344923,0.0110850709717964,0.942700102269306,0.674784989520932,1.27891869309046,0.000400957354522875,0.000201346292292629,0.000689191021815353,7.98617423460454,3.98540441782047,13.4351060178172,4.01310207644372,1.73587936049535,7.37912882550691,0.0138257653954597,1.01310207644372,PPV23 -France.post.PCV13,19A,1212,842076,2,8,16,adjusted_type_specific_poisson,0.00593521791438237,0.00366306350876752,0.00887295619924097,0.942700102269306,0.674784989520932,1.27891869309046,0.00193665997116141,0.00151058619668583,0.00243196471893208,7.19348411223143,4.43963297262623,10.7540229134801,17.7894942296201,11.5097418242099,25.5790263211395,0.806515887768566,1.78949422962011,PCV13 -France.post.PCV13,19F,1212,842076,2,6,7,adjusted_type_specific_poisson,0.00587402073070731,0.0031278183805729,0.00950732568631397,0.942700102269306,0.674784989520932,1.27891869309046,0.000752568056083617,0.000550123319373138,0.00100157805364369,7.11931312561726,3.79091587725435,11.5228787318125,6.84487384507424,3.62040750558201,11.1533507982895,1.11931312561726,0.155126154925759,PCV7 -France.post.PCV13,2,1212,842076,2,0,1,adjusted_type_specific_poisson,0.000350073095989733,9.66289309750223e-06,0.00164493544804452,0.942700102269306,0.674784989520932,1.27891869309046,0.00998959870125364,0.000295715381084731,0.0530573529119405,0.424288592339556,0.0117114264341727,1.99366176302995,1.55830708277535,0.15388946006506,4.6340974370674,0.424288592339556,0.558307082775347,PPV23 -France.post.PCV13,20,1212,842076,2,1,0,adjusted_type_specific_poisson,0.000804636696397068,8.73679648126944e-05,0.00244431795457803,0.942700102269306,0.674784989520932,1.27891869309046,0.000957797173992484,0.000238388518107766,0.00247568343665466,0.975219676033246,0.105889973352986,2.96251336094858,1.01634874086191,0.109797067350794,3.06465977913214,0.024780323966754,1.01634874086191,PPV23 -France.post.PCV13,21,1212,842076,2,3,3,adjusted_type_specific_poisson,0.0044593444512956,0.00175144006021905,0.00846777616868735,0.942700102269306,0.674784989520932,1.27891869309046,0.000234606065585659,0.00010602199615295,0.000423079520489989,5.40472547497027,2.12274535298549,10.2629447164491,1.59520564913269,0.526539828245004,3.44058867289125,2.40472547497027,1.40479435086731,No PCV -France.post.PCV13,22F,1212,842076,2,6,9,adjusted_type_specific_poisson,0.00547573463502765,0.00295046329769377,0.00896661832665,0.942700102269306,0.674784989520932,1.27891869309046,0.00111291794656347,0.000747288532056908,0.00157611065350571,6.63659037765351,3.57596151680485,10.8675414118998,9.34818868262288,5.11175527031583,14.8124796545918,0.636590377653507,0.348188682622876,PCV15 -France.post.PCV13,23A,1212,842076,2,9,4,adjusted_type_specific_poisson,0.00938797950130443,0.00512429620127355,0.014917163279362,0.942700102269306,0.674784989520932,1.27891869309046,0.00017858253466746,0.000100358645533425,0.000284446850590249,11.378231155581,6.21064699594354,18.0796018945868,2.59551165122056,1.18985478637715,4.67746780119463,2.37823115558097,1.40448834877944,No PCV -France.post.PCV13,23B,1212,842076,2,15,2,adjusted_type_specific_poisson,0.0108616682077273,0.00632752183401223,0.0166802031429008,0.942700102269306,0.674784989520932,1.27891869309046,0.000290469676688038,0.000174295346379655,0.000444118199022155,13.1643418677654,7.66895646282283,20.2164062091958,4.86979135434981,2.5452278960992,8.16935864721842,1.83565813223455,2.86979135434981,No PCV -France.post.PCV13,24A,1212,842076,2,1,1,adjusted_type_specific_poisson,0.0016353635439198,0.000199004937385636,0.00453784991363974,0.942700102269306,0.674784989520932,1.27891869309046,0.00078213866103892,1.09357719125262e-05,0.00432498968636224,1.98206061523079,0.24119398411139,5.49987409533136,1.01354778524813,0.0275656721412919,3.68625536530772,0.982060615230794,0.0135477852481349,No PCV -France.post.PCV13,24F,1212,842076,2,6,36,adjusted_type_specific_poisson,0.00765437621151215,0.00440142561697764,0.0119398336263399,0.942700102269306,0.674784989520932,1.27891869309046,0.00296592942741409,0.00168198604203905,0.00494246465975427,9.27710396835272,5.3345278477769,14.4710783551239,33.6199034928707,23.8975234068641,45.0055412852125,3.27710396835272,2.38009650712926,No PCV -France.post.PCV13,25A,1212,842076,2,1,0,adjusted_type_specific_poisson,0.000497128067850765,5.13638219246956e-05,0.00153263134546082,0.942700102269306,0.674784989520932,1.27891869309046,0.00205858895387132,0.0008321684683761,0.00449630852733197,0.602519218235128,0.062252952172731,1.85754919069851,1.40495730995852,0.165761009296564,4.02474932055997,0.397480781764872,1.40495730995852,No PCV -France.post.PCV13,29,1212,842076,2,1,1,adjusted_type_specific_poisson,0.00220524740621779,0.000431346582353302,0.00535044635081319,0.942700102269306,0.674784989520932,1.27891869309046,0.000105704622446372,3.26554376138359e-06,0.000442922821034247,2.67275985633597,0.522792057812201,6.48474097718559,0.323065709335085,0.00848802240208873,1.40275096656322,1.67275985633597,0.676934290664915,No PCV -France.post.PCV13,3,1212,842076,2,1,5,adjusted_type_specific_poisson,0.00155530830037744,0.000586576425719386,0.00304390360529209,0.942700102269306,0.674784989520932,1.27891869309046,0.00214630789735218,0.00150111695338643,0.00296037810122135,1.88503366005746,0.710930627971896,3.68921116961401,5.11136257360102,2.0201300667296,9.69785992149306,0.885033660057459,0.11136257360102,PCV13 -France.post.PCV13,31,1212,842076,2,2,1,adjusted_type_specific_poisson,0.0020132388305966,0.000512650235343342,0.00461875876881643,0.942700102269306,0.674784989520932,1.27891869309046,0.000529235275657269,0.000187950733188048,0.00110145716265855,2.44004546268308,0.621332085236131,5.59793562780551,1.54821430032718,0.351676028296208,3.72134459507207,0.440045462683077,0.548214300327178,No PCV -France.post.PCV13,33F,1212,842076,2,3,6,adjusted_type_specific_poisson,0.00288901357966715,0.00129631556025388,0.00526325633017943,0.942700102269306,0.674784989520932,1.27891869309046,0.00147980242560294,0.000904545029211608,0.00226255226693128,3.50148445855659,1.5711344590277,6.37906667217747,6.46487619555843,3.03779212736432,11.252743702606,0.501484458556587,0.464876195558431,PCV15 -France.post.PCV13,34,1212,842076,2,1,0,adjusted_type_specific_poisson,0.00144564989555941,0.000170126890183108,0.00409149136616259,0.942700102269306,0.674784989520932,1.27891869309046,0.000118248859863792,2.32905983534864e-05,0.000298872346256166,1.752127673418,0.206193790901927,4.95888753578906,0.254769087777499,0.0187594932587994,0.905651619282439,0.752127673418002,0.254769087777499,No PCV -France.post.PCV13,35B,1212,842076,2,7,4,adjusted_type_specific_poisson,0.00834345622369701,0.00430954699015594,0.0137197523663474,0.942700102269306,0.674784989520932,1.27891869309046,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,10.1122689431208,5.22317095206899,16.628339868013,1.85726141426909,0.726447969456272,3.6802576754999,3.11226894312077,2.14273858573091,No PCV -France.post.PCV13,35F,1212,842076,2,4,2,adjusted_type_specific_poisson,0.00468137267855598,0.00183763188304981,0.00885446634709174,0.942700102269306,0.674784989520932,1.27891869309046,0.000182256618407663,8.46996473232071e-05,0.000326715384700428,5.67382368640984,2.22720984225636,10.7316132126752,1.30766032846868,0.42618430122351,2.84705179831087,1.67382368640984,0.692339671531319,No PCV -France.post.PCV13,38,1212,842076,2,0,5,adjusted_type_specific_poisson,0.00213954501205952,0.00071072948542588,0.00448981983243605,0.942700102269306,0.674784989520932,1.27891869309046,0.00107630112860654,0.000517329118040196,0.00192400799311281,2.59312855461614,0.861404136336166,5.4416616369125,3.38206892981565,1.16072564670889,6.8199737414229,2.59312855461614,1.61793107018435,No PCV -France.post.PCV13,4,1212,842076,2,0,1,adjusted_type_specific_poisson,0.000404323317310844,4.57189136762859e-05,0.0011795680005473,0.942700102269306,0.674784989520932,1.27891869309046,0.00249105790199758,0.00143369758150515,0.00400799422771078,0.490039860580743,0.0554113233756585,1.42963641666333,1.49616779175024,0.180799678496142,4.21665437029512,0.490039860580743,0.496167791750238,PCV7 -France.post.PCV13,6A,1212,842076,2,0,1,adjusted_type_specific_poisson,0.00102934154379327,0.000123031560678575,0.00289889642042961,0.942700102269306,0.674784989520932,1.27891869309046,0.000470534749603847,0.000335293276070173,0.000638312814574088,1.24756195107744,0.149114251542432,3.51346246156069,0.75227306483863,0.0879196291141057,2.14585263376971,1.24756195107744,0.24772693516137,PCV13 -France.post.PCV13,6B,1212,842076,2,2,0,adjusted_type_specific_poisson,0.00124299670989563,0.000255160131582812,0.00304095173889954,0.942700102269306,0.674784989520932,1.27891869309046,0.000770579380902745,0.000565085521465747,0.00101866271810419,1.50651201239351,0.309254079478368,3.68563350754624,1.48475079315107,0.303478749629724,3.65303497235555,0.493487987606493,1.48475079315107,PCV7 -France.post.PCV13,6C,1212,842076,2,6,1,adjusted_type_specific_poisson,0.00581907599608496,0.00255197129946947,0.0104578457763179,0.942700102269306,0.674784989520932,1.27891869309046,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,7.05272010725497,3.092989214957,12.6749090808973,0.920206866428632,0.28826173463711,2.03464422089895,1.05272010725497,0.0797931335713677,No PCV -France.post.PCV13,7C,1212,842076,2,0,1,adjusted_type_specific_poisson,0.0010852750294552,0.000130370325391819,0.00313691823827271,0.942700102269306,0.674784989520932,1.27891869309046,0.000430538003690001,0.000121592824190092,0.000973102091763221,1.3153533356997,0.158008834374885,3.80194490478653,0.672275137930957,0.070661782385948,2.09975858775823,1.3153533356997,0.327724862069043,No PCV -France.post.PCV13,7F,1212,842076,2,1,0,adjusted_type_specific_poisson,0.000123138413150035,1.37810597452755e-05,0.000361789191646852,0.942700102269306,0.674784989520932,1.27891869309046,0.00997721126084835,0.00681051079664878,0.01416409744657,0.149243756737843,0.0167026444112739,0.438488500275985,1.85352035073541,0.22029628075245,5.23551052425109,0.850756243262157,1.85352035073541,PCV10 -France.post.PCV13,9N,1212,842076,2,1,0,adjusted_type_specific_poisson,0.000911980646438518,0.000103750764780796,0.00263273746615251,0.942700102269306,0.674784989520932,1.27891869309046,0.00065486417300752,0.000292518419108024,0.00122095961399422,1.10532054348348,0.125745926914325,3.19087780897684,0.884057974774682,0.097468045514366,2.59946777070935,0.105320543483484,0.884057974774682,PPV23 -Atlanta.post.PCV7,11A,451,298831,1,10,0,adjusted_type_specific_poisson,0.0233925818035888,0.0117542724496084,0.0388180083489625,0.703302645471613,0.444433552988253,1.05488067573423,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,10.5500543934186,5.30117687477338,17.5069217653821,0.414072612628951,0.146076246470547,0.884109933976811,0.550054393418568,0.414072612628951,PCV20 -Atlanta.post.PCV7,12F,451,298831,1,0,1,adjusted_type_specific_poisson,0.00105210385931892,0.000119431379165626,0.00316590774325822,0.703302645471613,0.444433552988253,1.05488067573423,0.00763701563010158,0.00413184393687895,0.0128667210227945,0.474498840552833,0.0538635520036973,1.42782439220946,1.5307934047147,0.183882382145979,4.27208537578922,0.474498840552833,0.530793404714703,PCV20 -Atlanta.post.PCV7,13,451,298831,1,0,1,adjusted_type_specific_poisson,0.00324109710289708,0.000398251516243955,0.00922561420246725,0.703302645471613,0.444433552988253,1.05488067573423,0.000869816776002311,0.000245481001501479,0.00212058387716859,1.46173479340658,0.179611433826024,4.16075200531273,0.53808525668403,0.0517185466110497,1.75129368090627,1.46173479340658,0.46191474331597,No PCV -Atlanta.post.PCV7,15A,451,298831,1,4,0,adjusted_type_specific_poisson,0.00921156056518671,0.0029416405113355,0.0191005862629126,0.703302645471613,0.444433552988253,1.05488067573423,0.000447893348168094,0.000276077603700969,0.000677854020290881,4.1544138148992,1.32667987061231,8.61436440457357,0.846048126362787,0.239340023827911,1.92612171682034,0.154413814899204,0.846048126362787,No PCV -Atlanta.post.PCV7,15B/C,451,298831,1,8,3,adjusted_type_specific_poisson,0.0222693553758222,0.0115040598350017,0.0365853191302859,0.703302645471613,0.444433552988253,1.05488067573423,0.000410284575081173,0.000285934443755961,0.000563977573171364,10.0434792744958,5.18833098558579,16.4999789277589,1.8839957180437,0.846593400551574,3.44595303611829,2.04347927449583,1.1160042819563,PCV20 -Atlanta.post.PCV7,19A,451,298831,1,29,23,adjusted_type_specific_poisson,0.0625808269150444,0.0445871682529957,0.083565539910543,0.703302645471613,0.444433552988253,1.05488067573423,0.00193665997116141,0.00151058619668583,0.00243196471893208,28.223952938685,20.1088128821011,37.6880584996549,24.7416933374461,17.1802791510353,33.9258204993225,0.776047061314951,1.74169333744608,PCV13 -Atlanta.post.PCV7,19F,451,298831,1,1,0,adjusted_type_specific_poisson,0.00330371662895148,0.000403227637355776,0.00920657730101418,0.703302645471613,0.444433552988253,1.05488067573423,0.000752568056083617,0.000550123319373138,0.00100157805364369,1.48997619965712,0.181855664447455,4.15216636275739,0.510981441133002,0.0581198907451659,1.45708244253861,0.489976199657117,0.510981441133002,PCV7 -Atlanta.post.PCV7,21,451,298831,1,3,2,adjusted_type_specific_poisson,0.0119407594942966,0.00439264141627695,0.023192838997728,0.703302645471613,0.444433552988253,1.05488067573423,0.000234606065585659,0.00010602199615295,0.000423079520489989,5.38528253192775,1.9810812787409,10.4599703879753,0.574421223822243,0.15711658378903,1.3684117973494,2.38528253192775,1.42557877617776,No PCV -Atlanta.post.PCV7,22F,451,298831,1,0,2,adjusted_type_specific_poisson,0.00440140392979401,0.000861352088184231,0.0107549205301962,0.703302645471613,0.444433552988253,1.05488067573423,0.00111291794656347,0.000747288532056908,0.00157611065350571,1.9850331723371,0.388469791771088,4.8504691591185,0.997191490463111,0.191942239684906,2.51547825910009,1.9850331723371,1.00280850953689,PCV15 -Atlanta.post.PCV7,23A,451,298831,1,10,0,adjusted_type_specific_poisson,0.0225148079185734,0.0113924014510142,0.037290417576723,0.703302645471613,0.444433552988253,1.05488067573423,0.00017858253466746,0.000100358645533425,0.000284446850590249,10.1541783712766,5.13797305440742,16.8179783271021,0.830077605986883,0.322339845684841,1.67262213445151,0.154178371276581,0.830077605986883,No PCV -Atlanta.post.PCV7,23B,451,298831,1,10,1,adjusted_type_specific_poisson,0.0234130348428299,0.0120008599079836,0.0384610165882107,0.703302645471613,0.444433552988253,1.05488067573423,0.000290469676688038,0.000174295346379655,0.000444118199022155,10.5592787141163,5.41238781850062,17.345918481283,1.4001137232999,0.585698710563707,2.67319252911096,0.559278714116278,0.400113723299901,No PCV -Atlanta.post.PCV7,3,451,298831,1,0,1,adjusted_type_specific_poisson,0.00226293569145382,0.000261345657734516,0.00641932115443994,0.703302645471613,0.444433552988253,1.05488067573423,0.00214630789735218,0.00150111695338643,0.00296037810122135,1.02058399684567,0.117866891638266,2.89511384065241,0.981256702239839,0.113910822869108,2.7775405895008,1.02058399684567,0.0187432977601611,PCV13 -Atlanta.post.PCV7,33F,451,298831,1,5,6,adjusted_type_specific_poisson,0.0159549940437732,0.00790612110090365,0.0271309002209728,0.703302645471613,0.444433552988253,1.05488067573423,0.00147980242560294,0.000904545029211608,0.00226255226693128,7.19570231374172,3.56566061650755,12.2360359996587,4.75079791089451,2.2166544804842,8.39892853955037,2.19570231374172,1.24920208910549,PCV15 -Atlanta.post.PCV7,35B,451,298831,1,14,1,adjusted_type_specific_poisson,0.0331508226199428,0.0190926502439031,0.0507869633975303,0.703302645471613,0.444433552988253,1.05488067573423,0.000144399285837605,6.74815031723523e-05,0.000256685569536053,14.9510210015942,8.61078526000028,22.9049204922862,0.985237458933593,0.372460561326023,2.00968038343741,0.951021001594208,0.014762541066407,No PCV -Atlanta.post.PCV7,38,451,298831,1,0,2,adjusted_type_specific_poisson,0.00447547774079832,0.000881696200564166,0.0109066546873583,0.703302645471613,0.444433552988253,1.05488067573423,0.00107630112860654,0.000517329118040196,0.00192400799311281,2.01844046110004,0.397644986454439,4.91890126399859,0.957242894979106,0.174745172478278,2.49590200503896,2.01844046110004,1.04275710502089,No PCV -Atlanta.post.PCV7,6C,451,298831,1,23,0,adjusted_type_specific_poisson,0.0507896208710313,0.0328281497459253,0.0728375513281867,0.703302645471613,0.444433552988253,1.05488067573423,0.000102244431670976,4.38951403188637e-05,0.000189967330494762,22.9061190128351,14.8054955354123,32.8497356490122,1.06654216314187,0.405809503062353,2.17697322855635,0.0938809871648907,1.06654216314187,No PCV -Atlanta.post.PCV7,7F,451,298831,1,0,4,adjusted_type_specific_poisson,0.00206433778290127,0.000609128778910357,0.00457896269774541,0.703302645471613,0.444433552988253,1.05488067573423,0.00997721126084835,0.00681051079664878,0.01416409744657,0.931016340088473,0.274717079288571,2.06511217668318,4.064784139034,1.31160528986365,8.36704383619032,0.931016340088473,0.0647841390340034,PCV10 -Atlanta.pre.PCV,11A,231,204680,1,5,0,adjusted_type_specific_poisson,0.0223767326587229,0.00820430455623852,0.0435146018406675,2.10064352560908,1.45465470246725,2.97695956951875,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,5.169025244165,1.8951943524911,10.0518730251942,0.803449230640446,0.243326715639588,1.8170296295854,0.169025244165,0.803449230640446,PCV20 -Atlanta.pre.PCV,14,231,204680,1,3,67,adjusted_type_specific_poisson,0.0315656788188656,0.021293531720526,0.0445245786360407,2.10064352560908,1.45465470246725,2.97695956951875,0.00486577684119951,0.00359593248342883,0.00641271837258626,7.29167180715795,4.9188058274415,10.2851776649254,63.5762178483708,49.5962682215115,79.2359172916518,4.29167180715795,3.42378215162919,PCV7 -Atlanta.pre.PCV,18C,231,204680,1,0,4,adjusted_type_specific_poisson,0.00308497892750226,0.000939435308605675,0.00678991181272112,2.10064352560908,1.45465470246725,2.97695956951875,0.00341462550925104,0.0021814214974022,0.00511035484325696,0.712630132253022,0.217009556287911,1.56846962873858,4.2752746193849,1.39850178326842,8.84382382181223,0.712630132253022,0.275274619384899,PCV7 -Atlanta.pre.PCV,19A,231,204680,1,8,9,adjusted_type_specific_poisson,0.0173964765554891,0.00959881718301359,0.0279352227395049,2.10064352560908,1.45465470246725,2.97695956951875,0.00193665997116141,0.00151058619668583,0.00243196471893208,4.01858608431799,2.21732676927614,6.45303645282564,14.0312848798206,8.29032245848962,21.3341437444669,3.98141391568201,5.03128487982063,PCV13 -Atlanta.pre.PCV,19F,231,204680,1,11,30,adjusted_type_specific_poisson,0.0759703493810269,0.0523704694083055,0.10443948178498,2.10064352560908,1.45465470246725,2.97695956951875,0.000752568056083617,0.000550123319373138,0.00100157805364369,17.5491507070172,12.0975784333186,24.1255202923303,23.8587441568762,16.6692141107396,32.4205748397709,6.54915070701722,6.1412558431238,PCV7 -Atlanta.pre.PCV,23F,231,204680,1,17,23,adjusted_type_specific_poisson,0.0738759597460319,0.0508178126185267,0.101559079444602,2.10064352560908,1.45465470246725,2.97695956951875,0.00077564137009531,0.000556479798610777,0.00105106918760042,17.0653467013334,11.7389147148797,23.460147351703,23.8801346178437,16.6958369019309,32.5488019643753,0.0653467013333611,0.880134617843698,PCV7 -Atlanta.pre.PCV,4,231,204680,1,0,10,adjusted_type_specific_poisson,0.00895072769318389,0.00380263307011637,0.0168466022270702,2.10064352560908,1.45465470246725,2.97695956951875,0.00249105790199758,0.00143369758150515,0.00400799422771078,2.06761809712548,0.87840823919688,3.89156511445321,8.9147540502816,4.33082292750396,15.1008447326342,2.06761809712548,1.0852459497184,PCV7 -Atlanta.pre.PCV,6A,231,204680,1,15,15,adjusted_type_specific_poisson,0.0721149288594694,0.0476824597703987,0.101845076110287,2.10064352560908,1.45465470246725,2.97695956951875,0.000470534749603847,0.000335293276070173,0.000638312814574088,16.6585485665374,11.0146482069621,23.5262125814764,14.1784487934891,9.2229875501669,20.3727915390471,1.65854856653744,0.821551206510893,PCV13 -Atlanta.pre.PCV,6B,231,204680,1,17,24,adjusted_type_specific_poisson,0.0758507389714566,0.0524167745490035,0.10396495842577,2.10064352560908,1.45465470246725,2.97695956951875,0.000770579380902745,0.000565085521465747,0.00101866271810419,17.5215207024065,12.1082749208198,24.0159053963529,24.4012590425838,17.1233757008939,32.9328642545579,0.521520702406484,0.401259042583757,PCV7 -Atlanta.pre.PCV,9V,231,204680,1,6,10,adjusted_type_specific_poisson,0.0133108500999426,0.0067402944847604,0.022865816771664,2.10064352560908,1.45465470246725,2.97695956951875,0.00259101673359874,0.00162148522659737,0.00391316735192488,3.07480637308674,1.55700802597965,5.28200367425437,13.9752921764707,8.04651496511597,21.5526141975118,2.92519362691326,3.97529217647072,PCV7 -Ontario.pre.PCV,11A,1139,580507,1,26,0,adjusted_type_specific_poisson,0.0233593104255985,0.0156444546138058,0.0325561364810133,0.301945646365954,0.206672577943382,0.429265967847269,8.56919534907728e-05,4.19586591562699e-05,0.000147219955445889,26.6062545747567,17.8190338051248,37.0814394518741,0.345714492010473,0.14868683353828,0.65943968632344,0.606254574756715,0.345714492010473,PCV20 -Ontario.pre.PCV,14,1139,580507,1,30,36,adjusted_type_specific_poisson,0.0338364681976054,0.0254871284310484,0.0434937905912614,0.301945646365954,0.206672577943382,0.429265967847269,0.00486577684119951,0.00359593248342883,0.00641271837258626,38.5397372770726,29.0298392829642,49.5394274834467,28.1208838523283,20.5065474606892,37.1578451766051,8.5397372770726,7.87911614767171,PCV7 -Ontario.pre.PCV,19A,1139,580507,1,16,2,adjusted_type_specific_poisson,0.0128853543794944,0.0077558083779329,0.019335912737874,0.301945646365954,0.206672577943382,0.429265967847269,0.00193665997116141,0.00151058619668583,0.00243196471893208,14.6764186382441,8.83386574246557,22.0236046084384,4.30285273368711,2.41606791645148,6.85789684831172,1.32358136175591,2.30285273368711,PCV13 -Ontario.pre.PCV,19F,1139,580507,1,71,9,adjusted_type_specific_poisson,0.0637261343795498,0.0506505531930262,0.0778951876153388,0.301945646365954,0.206672577943382,0.429265967847269,0.000752568056083617,0.000550123319373138,0.00100157805364369,72.5840670583072,57.6909800868568,88.7226186938709,8.25721894364138,5.60620212220738,11.5729994624537,1.58406705830721,0.742781056358623,PCV7 -Ontario.pre.PCV,23F,1139,580507,1,94,9,adjusted_type_specific_poisson,0.0817645467441054,0.0670930032954756,0.0978012059570934,0.301945646365954,0.206672577943382,0.429265967847269,0.00077564137009531,0.000556479798610777,0.00105106918760042,93.129818741536,76.4189307535467,111.395573585129,10.9078572302986,7.52711458782324,15.165520520644,0.870181258463973,1.90785723029861,PCV7 -Ontario.pre.PCV,6A,1139,580507,1,67,2,adjusted_type_specific_poisson,0.0573472713271986,0.0447364499528257,0.0712148491914377,0.301945646365954,0.206672577943382,0.429265967847269,0.000470534749603847,0.000335293276070173,0.000638312814574088,65.3185420416792,50.9548164962685,81.1137132290476,4.64959907960858,3.03392517344798,6.75803308419135,1.68145795832081,2.64959907960858,PCV13 -Ontario.pre.PCV,6B,1139,580507,1,108,11,adjusted_type_specific_poisson,0.0943659658405406,0.0786644273685841,0.111158625203341,0.301945646365954,0.206672577943382,0.429265967847269,0.000770579380902745,0.000565085521465747,0.00101866271810419,107.482835092376,89.5987827728173,126.609674106606,12.5154781378943,8.79434502682014,17.0478345600093,0.517164907624235,1.51547813789427,PCV7 -Morocco.pre.PCV,19A,200,212566,1,0,10,adjusted_type_specific_poisson,0.00720123480012158,0.00321750573232645,0.0132924505206002,3.40283134329234,2.10141564287832,5.29963406425802,0.00193665997116141,0.00151058619668583,0.00243196471893208,1.44024696002432,0.643501146465291,2.65849010412005,9.56337742392016,4.76511202414051,16.0253041745359,1.44024696002432,0.436622576079838,PCV13 -Morocco.pre.PCV,23A,200,212566,1,5,6,adjusted_type_specific_poisson,0.0368854916058168,0.0184448507453123,0.0621493154176526,3.40283134329234,2.10141564287832,5.29963406425802,0.00017858253466746,0.000100358645533425,0.000284446850590249,7.37709832116335,3.68897014906246,12.4298630835305,4.52671113161751,2.06972204052976,8.14258604351114,2.37709832116335,1.47328886838249,No PCV -Morocco.pre.PCV,23F,200,212566,1,3,11,adjusted_type_specific_poisson,0.0204233673876168,0.0103508615380936,0.0346546996543833,3.40283134329234,2.10141564287832,5.29963406425802,0.00077564137009531,0.000556479798610777,0.00105106918760042,4.08467347752337,2.07017230761871,6.93093993087666,10.8728424367452,6.0384024047723,17.2618999318902,1.08467347752337,0.127157563254823,PCV7 -Morocco.pre.PCV,3,200,212566,1,0,1,adjusted_type_specific_poisson,0.00121238660020225,0.000131830088359735,0.00359782344195019,3.40283134329234,2.10141564287832,5.29963406425802,0.00214630789735218,0.00150111695338643,0.00296037810122135,0.242477320040449,0.026366017671947,0.719564688390038,1.75888378421658,0.203313192316824,4.92594321433473,0.242477320040449,0.758883784216581,PCV13 -Morocco.pre.PCV,4,200,212566,1,1,0,adjusted_type_specific_poisson,0.0010926785411403,0.000111155772839344,0.0033836321802448,3.40283134329234,2.10141564287832,5.29963406425802,0.00249105790199758,0.00143369758150515,0.00400799422771078,0.218535708228059,0.0222311545678688,0.676726436048961,1.77949484076239,0.20130005728152,5.01386311750946,0.781464291771941,1.77949484076239,PCV7 -Morocco.pre.PCV,6A,200,212566,1,13,34,adjusted_type_specific_poisson,0.0902427886393017,0.0606771342610371,0.12598695490364,3.40283134329234,2.10141564287832,5.29963406425802,0.000470534749603847,0.000335293276070173,0.000638312814574088,18.0485577278603,12.1354268522074,25.197390980728,29.350152575163,20.7604352207657,39.6070220096913,5.04855772786033,4.649847424837,PCV13 -Morocco.pre.PCV,6B,200,212566,1,10,21,adjusted_type_specific_poisson,0.043906877044742,0.0263289414424102,0.0669331499566596,3.40283134329234,2.10141564287832,5.29963406425802,0.000770579380902745,0.000565085521465747,0.00101866271810419,8.7813754089484,5.26578828848203,13.3866299913319,23.2816525794092,15.593834113294,32.4935402939583,1.2186245910516,2.28165257940917,PCV7 -Morocco.pre.PCV,8,200,212566,1,1,0,adjusted_type_specific_poisson,0.00113124542685761,0.000119285944724521,0.00347911881118186,3.40283134329234,2.10141564287832,5.29963406425802,0.00244545634969096,0.00123914949735586,0.00432306004960451,0.226249085371522,0.0238571889449043,0.695823762236372,1.76458886920818,0.214930169931652,4.92807049188691,0.773750914628478,1.76458886920818,PCV20 +study,type,carriage_samples,surveillance_population,time_interval,carriage,disease,model_name,rho,rho_lower,rho_upper,delta,delta_lower,delta_upper,nu,nu_lower,nu_upper,phi,phi_lower,phi_upper,carriage_prediction,carriage_prediction_lower,carriage_prediction_upper,disease_prediction,disease_prediction_lower,disease_prediction_upper,carriage_rmse,disease_rmse,classification +Alabama.pre.PCV,1,827,19316,3.4,5,4,adjusted_type_specific_negbin,0.0054593125982254,0.00226660399088565,0.0114586740559469,1.33187421967662,0.639188851599072,2.79764843221233,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,4.51485151873241,1.87448150046243,9.47632344426805,8.12063513559167,3.00522908319448,22.0564051370665,0.485148481267591,4.12063513559167,PCV10 +Alabama.pre.PCV,13,827,19316,3.4,6,0,adjusted_type_specific_negbin,0.00757486054886237,0.00314615774300777,0.0147486782785115,1.33187421967662,0.639188851599072,2.79764843221233,0.000646064239496631,0.000179626011284756,0.00211440991216995,3.54405372684984,2.48735345296771,5.1992340148223,6.26440967390918,2.60187245346743,12.197156936329,0.420563563889229,0.0868692126664355,1.66436122166747,0.26440967390918,0.420563563889229,No PCV +Alabama.pre.PCV,14,827,19316,3.4,20,18,adjusted_type_specific_negbin,0.0275150459030484,0.0182719116574219,0.0395796627209514,1.33187421967662,0.639188851599072,2.79764843221233,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,22.754942961821,15.1108709406879,32.7323810702268,10.0902857552685,5.09945172614656,20.6014137688757,2.75494296182099,7.90971424473146,PCV7 +Alabama.pre.PCV,20,827,19316,3.4,3,0,adjusted_type_specific_negbin,0.00406699914836178,0.0012316588283693,0.00975525099050384,1.33187421967662,0.639188851599072,2.79764843221233,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,3.3634082956952,1.01858185106141,8.06759256914667,0.269729048061298,0.0456855016954468,1.2144610748245,0.363408295695195,0.269729048061298,PPV23 +Alabama.pre.PCV,3,827,19316,3.4,35,0,adjusted_type_specific_negbin,0.0402189970281285,0.0283168257855183,0.0550995377978993,1.33187421967662,0.639188851599072,2.79764843221233,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,33.2611105422623,23.4180149246236,45.5673177588628,7.11277191312091,3.16082980677044,16.4963103553944,1.73888945773769,7.11277191312091,PCV13 +Alabama.pre.PCV,31,827,19316,3.4,0,1,adjusted_type_specific_negbin,0.0018982427747034,0.000275732055885754,0.00629520048873631,1.33187421967662,0.639188851599072,2.79764843221233,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,1.56984677467971,0.228030410217518,5.20613080418493,0.0776784365280474,0.00902514383858386,0.404167167373058,1.56984677467971,0.922321563471953,No PCV +Alabama.pre.PCV,37,827,19316,3.4,13,0,adjusted_type_specific_negbin,0.0163302276448635,0.00914029660773075,0.0264864829356566,1.33187421967662,0.639188851599072,2.79764843221233,8.82466692072548e-05,4.22185054013693e-06,0.000564483172719643,3.54405372684984,2.48735345296771,5.1992340148223,13.5050982623021,7.55902529459333,21.904321387788,0.123674110437649,0.00573856073430592,0.877893272411792,0.505098262302148,0.123674110437649,No PCV +Alabama.pre.PCV,38,827,19316,3.4,3,0,adjusted_type_specific_negbin,0.00404725570791597,0.00119202751478415,0.0097708170633709,1.33187421967662,0.639188851599072,2.79764843221233,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,3.3470804704465,0.985806754726491,8.08046571140774,0.304515315209165,0.0666894699913544,1.12017400494308,0.347080470446503,0.304515315209165,No PCV +Alabama.pre.PCV,4,827,19316,3.4,14,8,adjusted_type_specific_negbin,0.0205179924924595,0.0126520226753756,0.0313162574601786,1.33187421967662,0.639188851599072,2.79764843221233,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,16.968379791264,10.4632227525356,25.8985449195677,3.40392086898689,1.50569475897383,7.5891467463421,2.96837979126402,4.59607913101311,PCV7 +Alabama.pre.PCV,5,827,19316,3.4,0,1,adjusted_type_specific_negbin,0.00111434743517435,0.000148716305278314,0.00421800094210342,1.33187421967662,0.639188851599072,2.79764843221233,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,0.921565328889191,0.122988384465165,3.48828677911953,0.69872817402109,0.0890392204037466,3.12565589073763,0.921565328889191,0.30127182597891,PCV10 +Alabama.pre.PCV,8,827,19316,3.4,4,0,adjusted_type_specific_negbin,0.00482074814644516,0.00164038751218879,0.0108280281221477,1.33187421967662,0.639188851599072,2.79764843221233,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,3.98675871711015,1.35660047258013,8.95477925701618,0.792418778422421,0.20997951380223,2.59802691303999,0.013241282889854,0.792418778422421,PCV20 +Barcelona.post.PCV7,1,209,228000,4,2,39,adjusted_type_specific_negbin,0.015237555891788,0.00643140906197525,0.0325104873694377,0.154819298518161,0.094169708974972,0.254400430900583,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,3.1846491813837,1.34416449395283,6.79469186021249,36.4464876087308,16.8295652681587,84.1388877771819,1.1846491813837,2.55351239126915,PCV10 +Barcelona.post.PCV7,10A,209,228000,4,10,2,adjusted_type_specific_negbin,0.0457152950402321,0.0244400149697151,0.0777674542009403,0.154819298518161,0.094169708974972,0.254400430900583,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,9.5544966634085,5.10796312867046,16.2533979279965,4.59961890991373,2.04583077032841,9.99832718023823,0.4455033365915,2.59961890991373,PCV20 +Barcelona.post.PCV7,11A,209,228000,4,9,0,adjusted_type_specific_negbin,0.044208708975488,0.0222291435669801,0.076401028080061,0.154819298518161,0.094169708974972,0.254400430900583,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,9.23962017587699,4.64589100549883,15.9678148687328,0.415436568720356,0.146545979432811,1.03252411017814,0.239620175876993,0.415436568720356,PCV20 +Barcelona.post.PCV7,14,209,228000,4,4,6,adjusted_type_specific_negbin,0.0176559467011111,0.00713142654112392,0.0380866447624621,0.154819298518161,0.094169708974972,0.254400430900583,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,3.69009286053222,1.4904681470949,7.96010875535457,10.4620067975773,4.16939141675355,24.8009064782672,0.30990713946778,4.46200679757733,PCV7 +Barcelona.post.PCV7,15A,209,228000,4,6,2,adjusted_type_specific_negbin,0.0321679726776284,0.0144095381074944,0.0602032004065487,0.154819298518161,0.094169708974972,0.254400430900583,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,6.72310628962433,3.01159346446633,12.5824688849687,1.85646387116469,0.727998232886302,4.51157667337781,0.723106289624328,0.143536128835305,No PCV +Barcelona.post.PCV7,15B/C,209,228000,4,13,3,adjusted_type_specific_negbin,0.0648333576995351,0.0379428885887346,0.10192206248461,0.154819298518161,0.094169708974972,0.254400430900583,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,13.5501717592028,7.93006371504552,21.3017110592835,3.17362673754482,1.55558716899217,6.2821670262576,0.550171759202829,0.173626737544821,PCV20 +Barcelona.post.PCV7,16F,209,228000,4,5,2,adjusted_type_specific_negbin,0.0283293025032204,0.0123786557327398,0.0546040760774827,0.154819298518161,0.094169708974972,0.254400430900583,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,5.92082422317306,2.58713904814261,11.4122519001939,1.55991013712828,0.562427525632758,3.89283798797123,0.92082422317306,0.440089862871718,No PCV +Barcelona.post.PCV7,17F,209,228000,4,5,0,adjusted_type_specific_negbin,0.0228160352255288,0.00856604805491075,0.0474756374046759,0.154819298518161,0.094169708974972,0.254400430900583,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,4.76855136213551,1.79030404347635,9.92240821757727,1.21479165945476,0.369496438136394,3.41255897486299,0.231448637864485,1.21479165945476,PPV23 +Barcelona.post.PCV7,19A,209,228000,4,21,34,adjusted_type_specific_negbin,0.108969040603191,0.0742739842227158,0.15333888971813,0.154819298518161,0.094169708974972,0.254400430900583,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,22.774529486067,15.5232627025476,32.0478279510891,23.6455489663466,13.8422230623432,40.9197884360843,1.774529486067,10.3544510336534,PCV13 +Barcelona.post.PCV7,19F,209,228000,4,13,7,adjusted_type_specific_negbin,0.0668930238350438,0.0403998101587328,0.103596517126413,0.154819298518161,0.094169708974972,0.254400430900583,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,13.9806419815241,8.44356032317515,21.6516720794204,6.02502276389223,3.15162846096308,11.4399856744427,0.980641981524148,0.974977236107766,PCV7 +Barcelona.post.PCV7,21,209,228000,4,5,0,adjusted_type_specific_negbin,0.0242519482512921,0.00936280919328977,0.0497793509287623,0.154819298518161,0.094169708974972,0.254400430900583,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,5.06865718452006,1.95682712139756,10.4038843441113,0.67536082653606,0.195714093119914,1.94193506972336,0.0686571845200579,0.67536082653606,No PCV +Barcelona.post.PCV7,22F,209,228000,4,8,3,adjusted_type_specific_negbin,0.0372555966598062,0.0183609683133888,0.0662819021630035,0.154819298518161,0.094169708974972,0.254400430900583,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,7.7864197018995,3.83744237749826,13.8529175520677,5.32942643025891,2.33191336863915,11.8832741193931,0.213580298100502,2.32942643025891,PCV15 +Barcelona.post.PCV7,23A,209,228000,4,9,0,adjusted_type_specific_negbin,0.0424770313573768,0.0210050181090965,0.0748752040559268,0.154819298518161,0.094169708974972,0.254400430900583,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,8.87769955369176,4.39004878480117,15.6489176476887,0.944083452790729,0.362736370229754,2.24429437344932,0.122300446308238,0.944083452790729,No PCV +Barcelona.post.PCV7,23B,209,228000,4,17,5,adjusted_type_specific_negbin,0.088183490072465,0.0564701036038471,0.129438676842879,0.154819298518161,0.094169708974972,0.254400430900583,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,18.4303494251452,11.802251653204,27.0526834601617,3.19445329964217,1.5589024773979,6.42932294389982,1.43034942514518,1.80554670035783,No PCV +Barcelona.post.PCV7,23F,209,228000,4,7,4,adjusted_type_specific_negbin,0.0374878785813887,0.0189398314998112,0.0661114256566856,0.154819298518161,0.094169708974972,0.254400430900583,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,7.83496662351024,3.95842478346053,13.8172879622473,3.62370235340626,1.64047365123225,7.52638371430882,0.834966623510245,0.37629764659374,PCV7 +Barcelona.post.PCV7,3,209,228000,4,2,8,adjusted_type_specific_negbin,0.0185176969070287,0.00790953697451245,0.0377311018514338,0.154819298518161,0.094169708974972,0.254400430900583,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,3.870198653569,1.6530932276731,7.88580028694966,5.27244639959723,2.2548303780774,11.6714154172518,1.870198653569,2.72755360040277,PCV13 +Barcelona.post.PCV7,34,209,228000,4,6,0,adjusted_type_specific_negbin,0.0298826519806693,0.0127117061013663,0.0579245477607901,0.154819298518161,0.094169708974972,0.254400430900583,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,6.24547426395989,2.65674657518555,12.1062304820051,0.410965939585768,0.076687309160096,1.5843458820915,0.245474263959887,0.410965939585768,No PCV +Barcelona.post.PCV7,35B,209,228000,4,5,0,adjusted_type_specific_negbin,0.0249768093679877,0.00988707530837582,0.0504953565480292,0.154819298518161,0.094169708974972,0.254400430900583,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,5.22015315790944,2.06639873945055,10.5535295185381,0.450817814817646,0.134801094453168,1.30125391634485,0.220153157909438,0.450817814817646,No PCV +Barcelona.post.PCV7,5,209,228000,4,0,14,adjusted_type_specific_negbin,0.00971905259705422,0.00322461933104373,0.0240643076495161,0.154819298518161,0.094169708974972,0.254400430900583,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,2.03128199278433,0.67394544018814,5.02944029874887,9.75078456870569,4.0557250060837,24.9320864352186,2.03128199278433,4.24921543129431,PCV10 +Barcelona.post.PCV7,6A,209,228000,4,16,4,adjusted_type_specific_negbin,0.078175727264192,0.0477700302725201,0.117554703439974,0.154819298518161,0.094169708974972,0.254400430900583,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,16.3387269982161,9.9839363269567,24.5689330189546,4.75174896001601,2.42242831030202,9.11392562595011,0.338726998216121,0.751748960016005,PCV13 +Barcelona.post.PCV7,6B,209,228000,4,4,2,adjusted_type_specific_negbin,0.0216870525218069,0.00877099174970725,0.0441328115797429,0.154819298518161,0.094169708974972,0.254400430900583,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,4.53259397705764,1.83313727568882,9.22375762016627,2.27474844526652,0.852338910193248,5.36897193811175,0.532593977057639,0.274748445266519,PCV7 +Barcelona.post.PCV7,6C,209,228000,4,19,1,adjusted_type_specific_negbin,0.0929525545847917,0.0592772696833468,0.136772148622817,0.154819298518161,0.094169708974972,0.254400430900583,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,19.4270839082215,12.3889493638195,28.5853790621688,1.08721952091486,0.403605477398765,2.71146653632965,0.427083908221462,0.0872195209148618,No PCV +Barcelona.post.PCV7,7F,209,228000,4,0,14,adjusted_type_specific_negbin,0.00820132847728496,0.00303502539184919,0.020236965575801,0.154819298518161,0.094169708974972,0.254400430900583,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,1.71407765175256,0.63432030689648,4.2295258053424,10.9025441689628,4.44541439544358,26.7043900452173,1.71407765175256,3.09745583103715,PCV10 +Bogota.post.PCV7,1,246,357200,1,0,8,adjusted_type_specific_negbin,0.00237645132057168,0.000655255416170949,0.00830800986803236,0.661676656405915,0.389522764969488,1.12658025519891,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,0.584607024860634,0.161192832378053,2.04377042753596,9.61351861291016,3.08527382371298,32.3540640452957,0.584607024860634,1.61351861291016,PCV10 +Bogota.post.PCV7,10A,246,357200,1,1,0,adjusted_type_specific_negbin,0.00440801366098229,0.000582002970472124,0.0154150883881439,0.661676656405915,0.389522764969488,1.12658025519891,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,1.08437136060164,0.143172730736142,3.79211174348339,0.738871526046887,0.097943770144715,2.81239411123728,0.0843713606016445,0.738871526046887,PCV20 +Bogota.post.PCV7,11A,246,357200,1,7,2,adjusted_type_specific_negbin,0.0359098614349791,0.0179289930205092,0.0631338685151593,0.661676656405915,0.389522764969488,1.12658025519891,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,8.83382591300485,4.41053228304526,15.5309316547292,0.563378962873701,0.201607218424278,1.38793003740214,1.83382591300485,1.4366210371263,PCV20 +Bogota.post.PCV7,13,246,357200,1,1,0,adjusted_type_specific_negbin,0.00445721640679353,0.000605174648868708,0.0160725567869435,0.661676656405915,0.389522764969488,1.12658025519891,0.000646064239496631,0.000179626011284756,0.00211440991216995,3.54405372684984,2.48735345296771,5.1992340148223,1.09647523607121,0.148872963621702,3.95384896958811,0.660878934762181,0.0809161221321319,3.19667747505242,0.0964752360712076,0.660878934762181,No PCV +Bogota.post.PCV7,14,246,357200,1,3,14,adjusted_type_specific_negbin,0.0149685744449207,0.00644492630442069,0.0314284764454548,0.661676656405915,0.389522764969488,1.12658025519891,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,3.68226931345049,1.58545187088749,7.73140520558187,14.8497260630641,6.501038608747,33.9589066983778,0.682269313450489,0.849726063064114,PCV7 +Bogota.post.PCV7,15A,246,357200,1,2,2,adjusted_type_specific_negbin,0.0130248043720159,0.00432542074609678,0.0298817043468423,0.661676656405915,0.389522764969488,1.12658025519891,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,3.2041018755159,1.06405350353981,7.3508992693232,1.2690149322964,0.391472143606079,3.46613668293194,1.2041018755159,0.730985067703599,No PCV +Bogota.post.PCV7,15B/C,246,357200,1,13,5,adjusted_type_specific_negbin,0.0560223646524581,0.0329118972640147,0.0879650060189447,0.661676656405915,0.389522764969488,1.12658025519891,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,13.7815017045047,8.09632672694761,21.6393914806604,4.59878913826942,2.25254331399674,9.16291385483753,0.781501704504699,0.401210861730582,PCV20 +Bogota.post.PCV7,16F,246,357200,1,1,2,adjusted_type_specific_negbin,0.0102017483985722,0.00287020128246193,0.0253434157776356,0.661676656405915,0.389522764969488,1.12658025519891,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,2.50963010604875,0.706069515485634,6.23448028129836,0.945603022994197,0.242282292584868,2.82622434009267,1.50963010604875,1.0543969770058,No PCV +Bogota.post.PCV7,17F,246,357200,1,2,0,adjusted_type_specific_negbin,0.0083936316258422,0.00187508660823116,0.0236648645852985,0.661676656405915,0.389522764969488,1.12658025519891,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,2.06483337995718,0.461271305624866,5.82155668798343,0.747481060393317,0.146629875604685,2.60656881432439,0.0648333799571823,0.747481060393317,PPV23 +Bogota.post.PCV7,18A,246,357200,1,1,0,adjusted_type_specific_negbin,0.00564223725795016,0.000791946076422167,0.0191969415850149,0.661676656405915,0.389522764969488,1.12658025519891,0.000199167672918468,2.36758150914551e-05,0.00102580832813065,3.54405372684984,2.48735345296771,5.1992340148223,1.38799036545574,0.194818734799853,4.72244762991366,0.249478859376095,0.0176296046297206,1.65409327167401,0.38799036545574,0.249478859376095,No PCV +Bogota.post.PCV7,18C,246,357200,1,2,5,adjusted_type_specific_negbin,0.00972501162526782,0.00338356263794172,0.0238401073066056,0.661676656405915,0.389522764969488,1.12658025519891,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,2.39235285981588,0.832356408933663,5.86466639742498,6.15509072665061,2.18606150843252,16.7833404490536,0.392352859815884,1.15509072665061,PCV7 +Bogota.post.PCV7,19A,246,357200,1,3,5,adjusted_type_specific_negbin,0.0147354721169023,0.00597535560909664,0.0309992334927588,0.661676656405915,0.389522764969488,1.12658025519891,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,3.62492614075796,1.46993747983777,7.62581143921866,5.32864488839476,2.1546421123314,12.3730680481252,0.624926140757963,0.328644888394761,PCV13 +Bogota.post.PCV7,19B,246,357200,1,1,0,adjusted_type_specific_negbin,0.00643601696380802,0.000902372880761939,0.0212383965067233,0.661676656405915,0.389522764969488,1.12658025519891,1.18969542866196e-05,1.13237127398798e-06,0.000461834995257341,3.54405372684984,2.48735345296771,5.1992340148223,1.58326017309677,0.221983728667437,5.22464554065394,0.0177773425524987,0.00076146563551284,0.690842990890049,0.583260173096772,0.0177773425524987,No PCV +Bogota.post.PCV7,19F,246,357200,1,3,2,adjusted_type_specific_negbin,0.0145541617134226,0.00524890370917865,0.0319791171905068,0.661676656405915,0.389522764969488,1.12658025519891,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,3.58032378150196,1.29123031245795,7.86686282886468,2.18870854132123,0.746810017553139,5.50712283168654,0.580323781501955,0.188708541321231,PCV7 +Bogota.post.PCV7,20,246,357200,1,0,1,adjusted_type_specific_negbin,0.00378222012497263,0.000451314603414642,0.0144872411785396,0.661676656405915,0.389522764969488,1.12658025519891,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,0.930426150743266,0.111023392440002,3.56386132992073,0.666365766243272,0.0799900505833565,3.13745596705527,0.930426150743266,0.333634233756728,PPV23 +Bogota.post.PCV7,22F,246,357200,1,0,1,adjusted_type_specific_negbin,0.00346150118754445,0.000449159030401246,0.012735474495128,0.661676656405915,0.389522764969488,1.12658025519891,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,0.851529292135935,0.110493121478707,3.13292672580148,0.832914633476985,0.111745030750482,3.26240958870812,0.851529292135935,0.167085366523015,PCV15 +Bogota.post.PCV7,23A,246,357200,1,6,0,adjusted_type_specific_negbin,0.0241855517358934,0.0103137906231596,0.0470068980654696,0.661676656405915,0.389522764969488,1.12658025519891,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,5.94964572702978,2.53719249329727,11.5636969241055,0.903607888867809,0.3046515147452,2.2891432770669,0.0503542729702247,0.903607888867809,No PCV +Bogota.post.PCV7,23B,246,357200,1,1,1,adjusted_type_specific_negbin,0.00842388265329027,0.00191322018044483,0.023306847224296,0.661676656405915,0.389522764969488,1.12658025519891,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,2.07227513270941,0.470652164389427,5.73348441717683,0.509623397275062,0.106270090219044,1.65924700927272,1.07227513270941,0.490376602724938,No PCV +Bogota.post.PCV7,23F,246,357200,1,5,4,adjusted_type_specific_negbin,0.0235356273098975,0.0106109314891261,0.0451745738483082,0.661676656405915,0.389522764969488,1.12658025519891,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,5.78976431823479,2.61028914632502,11.1129451666838,3.8048004075104,1.60427171650853,8.47446121330311,0.789764318234791,0.195199592489605,PCV7 +Bogota.post.PCV7,24F,246,357200,1,1,1,adjusted_type_specific_negbin,0.00422258513485191,0.000840966406709049,0.0141322683414043,0.661676656405915,0.389522764969488,1.12658025519891,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,1.03875594317357,0.206877736050426,3.47653801198546,2.15762642095314,0.444145208271784,7.92154568221002,0.0387559431735696,1.15762642095314,No PCV +Bogota.post.PCV7,25A,246,357200,1,0,3,adjusted_type_specific_negbin,0.00536622633494213,0.00123145669523738,0.0163507695243028,0.661676656405915,0.389522764969488,1.12658025519891,0.00163929978568756,0.000579341956760081,0.00489291543751703,3.54405372684984,2.48735345296771,5.1992340148223,1.32009167839576,0.302938347028396,4.0222893029785,2.0370529113223,0.517743073006126,6.77908816443561,1.32009167839576,0.962947088677704,No PCV +Bogota.post.PCV7,28A,246,357200,1,0,2,adjusted_type_specific_negbin,0.00277940051729231,0.00010037805872734,0.0148159711323718,0.661676656405915,0.389522764969488,1.12658025519891,0.00298450280669115,0.000170948103836682,0.117079819057643,3.54405372684984,2.48735345296771,5.1992340148223,0.683732527253909,0.0246930024469257,3.64472889856346,1.87053982258795,0.21432105738766,11.4997409532841,0.683732527253909,0.129460177412053,No PCV +Bogota.post.PCV7,29,246,357200,1,1,0,adjusted_type_specific_negbin,0.00618718494486456,0.000857621075276873,0.0209165089896063,0.661676656405915,0.389522764969488,1.12658025519891,6.4477890005963e-05,3.10034323663527e-06,0.000486340435351969,3.54405372684984,2.48735345296771,5.1992340148223,1.52204749643668,0.210974784518111,5.14546121144315,0.0850075366947692,0.00300671890657394,0.888788431941976,0.522047496436681,0.0850075366947692,No PCV +Bogota.post.PCV7,3,246,357200,1,1,12,adjusted_type_specific_negbin,0.0144999346548346,0.00612207890140598,0.0297997651016943,0.661676656405915,0.389522764969488,1.12658025519891,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,3.56698392508932,1.50603140974587,7.3307422150168,6.91230345166618,3.06191008017087,15.0268188619769,2.56698392508932,5.08769654833382,PCV13 +Bogota.post.PCV7,35B,246,357200,1,5,2,adjusted_type_specific_negbin,0.0265690493713543,0.0119322371757536,0.0502468950526884,0.661676656405915,0.389522764969488,1.12658025519891,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,6.53598614535316,2.93533034523538,12.3607361829613,0.809940398812666,0.269348617736526,2.13684638747838,1.53598614535316,1.19005960118733,No PCV +Bogota.post.PCV7,35F,246,357200,1,3,0,adjusted_type_specific_negbin,0.0131131484959341,0.00394665831194448,0.0315486738806579,0.661676656405915,0.389522764969488,1.12658025519891,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,3.2258345299998,0.970877944738343,7.76097377464183,0.457099811164119,0.110460057395945,1.46311651940619,0.225834529999796,0.457099811164119,No PCV +Bogota.post.PCV7,4,246,357200,1,0,1,adjusted_type_specific_negbin,0.00256909346188139,0.000334604264178532,0.0104156907444768,0.661676656405915,0.389522764969488,1.12658025519891,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,0.631996991622822,0.0823126489879189,2.56225992314129,1.14759686192963,0.151520313920425,4.81442174312774,0.631996991622822,0.147596861929626,PCV7 +Bogota.post.PCV7,42,246,357200,1,1,0,adjusted_type_specific_negbin,0.00637257957339055,0.000885631047029949,0.0215188739585347,0.661676656405915,0.389522764969488,1.12658025519891,1.66572113216006e-05,1.16494987530368e-06,0.000762582274495337,3.54405372684984,2.48735345296771,5.1992340148223,1.56765457505408,0.217865237569367,5.29364299379952,0.0245598816274526,0.000804383304044019,1.04729404656346,0.567654575054076,0.0245598816274526,No PCV +Bogota.post.PCV7,5,246,357200,1,0,1,adjusted_type_specific_negbin,0.00107326145235396,0.000109299622652559,0.00596117636204736,0.661676656405915,0.389522764969488,1.12658025519891,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,0.264022317279074,0.0268877071725296,1.46644938506365,1.84351886801191,0.22092875335197,9.7208279828845,0.264022317279074,0.843518868011914,PCV10 +Bogota.post.PCV7,6A,246,357200,1,6,1,adjusted_type_specific_negbin,0.0237326426160327,0.0104724437554678,0.0461115037274806,0.661676656405915,0.389522764969488,1.12658025519891,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,5.83823008354404,2.57622116384507,11.3434299169602,2.41110140203084,0.947519138132663,5.64501003552207,0.161769916455958,1.41110140203084,PCV13 +Bogota.post.PCV7,6B,246,357200,1,2,4,adjusted_type_specific_negbin,0.0144235704778882,0.00556148248609279,0.0313914461767118,0.661676656405915,0.389522764969488,1.12658025519891,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,3.5481983375605,1.36812469157883,7.72229575947109,2.53804034758275,0.947255974672176,6.15161236520935,1.5481983375605,1.46195965241725,PCV7 +Bogota.post.PCV7,6C,246,357200,1,2,0,adjusted_type_specific_negbin,0.00992215731452589,0.00231809392147555,0.0270400185058292,0.661676656405915,0.389522764969488,1.12658025519891,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,2.44085069937337,0.570251104682985,6.65184455243399,0.192250151983943,0.0358637256923787,0.729727452136095,0.44085069937337,0.192250151983943,No PCV +Bogota.post.PCV7,7C,246,357200,1,1,0,adjusted_type_specific_negbin,0.0050651111917131,0.000693352623280182,0.0176487581439701,0.661676656405915,0.389522764969488,1.12658025519891,0.000393012283852677,0.00011306744230165,0.00121318243232636,3.54405372684984,2.48735345296771,5.1992340148223,1.24601735316142,0.170564745326925,4.34159450341665,0.455408203194364,0.0507232201826962,2.22359061405349,0.246017353161422,0.455408203194364,No PCV +Bogota.post.PCV7,8,246,357200,1,0,2,adjusted_type_specific_negbin,0.00382689366614939,0.000748875207549962,0.0132186565116552,0.661676656405915,0.389522764969488,1.12658025519891,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,0.94141584187275,0.184223301057291,3.25178950186718,1.72064544864297,0.347927479453963,6.15587596670671,0.94141584187275,0.279354551357029,PCV20 +Bogota.post.PCV7,9V,246,357200,1,0,2,adjusted_type_specific_negbin,0.00371862695448471,0.000735263778576405,0.0125820975962803,0.661676656405915,0.389522764969488,1.12658025519891,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,0.91478223080324,0.180874889529796,3.09519600868496,1.78882170699082,0.372678652321902,6.23161646333669,0.91478223080324,0.211178293009179,PCV7 +Bogota.pre.PCV,1,197,357200,4,0,29,adjusted_type_specific_negbin,0.00515207747001812,0.00178877113424073,0.0142709897132266,0.234465653537149,0.145831387105995,0.380725815830876,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,1.01495926159357,0.352387913445423,2.81138497350565,29.5210506701053,11.8482348952753,80.8602497644823,1.01495926159357,0.521050670105332,PCV10 +Bogota.pre.PCV,10A,197,357200,4,3,1,adjusted_type_specific_negbin,0.013159924969611,0.00411864800901074,0.0326105378725766,0.234465653537149,0.145831387105995,0.380725815830876,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,2.59250521901337,0.811373657775115,6.42427596089759,3.13435422914605,0.938272816099428,8.70043036590464,0.407494780986626,2.13435422914605,PCV20 +Bogota.pre.PCV,10B,197,357200,4,0,1,adjusted_type_specific_negbin,0.00437224511955902,0.000521495177031532,0.0178574768867653,0.234465653537149,0.145831387105995,0.380725815830876,0.000502204985915827,8.47222594103277e-05,0.00253825696624574,3.54405372684984,2.48735345296771,5.1992340148223,0.861332288553127,0.102734549875212,3.51792294669276,0.711271628881474,0.0748356516814909,3.70888690865948,0.861332288553127,0.288728371118526,No PCV +Bogota.pre.PCV,11A,197,357200,4,4,1,adjusted_type_specific_negbin,0.025382965857855,0.00999805568311514,0.0516619099812858,0.234465653537149,0.145831387105995,0.380725815830876,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,5.00044427399743,1.96961696957368,10.1773962663133,0.562923920256148,0.17797288877527,1.49656866565453,1.00044427399743,0.437076079743852,PCV20 +Bogota.pre.PCV,12F,197,357200,4,0,3,adjusted_type_specific_negbin,0.00204505048288435,0.00038959408229298,0.00858764790451694,0.234465653537149,0.145831387105995,0.380725815830876,0.00604172772796168,0.00276457252642332,0.013992691352501,3.54405372684984,2.48735345296771,5.1992340148223,0.402874945128218,0.076750034211717,1.69176663718984,4.09973104242749,0.94091617289211,16.5455922939461,0.402874945128218,1.09973104242749,PCV20 +Bogota.pre.PCV,13,197,357200,4,1,4,adjusted_type_specific_negbin,0.0125304442308817,0.00374307602400472,0.0316162493796045,0.234465653537149,0.145831387105995,0.380725815830876,0.000646064239496631,0.000179626011284756,0.00211440991216995,3.54405372684984,2.48735345296771,5.1992340148223,2.4684975134837,0.737385976728929,6.22840112778208,2.60436338408804,0.744501786724782,8.46028405924671,1.4684975134837,1.39563661591196,No PCV +Bogota.pre.PCV,14,197,357200,4,9,163,adjusted_type_specific_negbin,0.0632456392914673,0.0386814451948294,0.0975602937865779,0.234465653537149,0.145831387105995,0.380725815830876,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,12.4593909404191,7.62024470338139,19.2193778759559,88.9888120843141,52.0515876595137,155.496790903242,3.45939094041906,74.0111879156859,PCV7 +Bogota.pre.PCV,15A,197,357200,4,0,1,adjusted_type_specific_negbin,0.00492175079216769,0.000675179012572713,0.0177345327779226,0.234465653537149,0.145831387105995,0.380725815830876,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,0.969584906057034,0.133010265476824,3.49370295725076,0.680957777814931,0.0949943090498459,2.60611818508212,0.969584906057034,0.319042222185069,No PCV +Bogota.pre.PCV,15B/C,197,357200,4,6,2,adjusted_type_specific_negbin,0.0301182039908677,0.0134366897972022,0.057596994628159,0.234465653537149,0.145831387105995,0.380725815830876,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,5.93328618620095,2.64702789004883,11.3466079417473,3.49208177840053,1.41488236943097,7.82618094242518,0.0667138137990548,1.49208177840053,PCV20 +Bogota.pre.PCV,15F,197,357200,4,1,0,adjusted_type_specific_negbin,0.00655613787616765,0.000876463384165064,0.0233498610103991,0.234465653537149,0.145831387105995,0.380725815830876,0.000169416469056684,1.99360904401105e-05,0.000839805104163891,3.54405372684984,2.48735345296771,5.1992340148223,1.29155916160503,0.172663286680518,4.59992261904863,0.348996785349369,0.0242162190873416,2.2466497051655,0.291559161605027,0.348996785349369,No PCV +Bogota.pre.PCV,16F,197,357200,4,1,3,adjusted_type_specific_negbin,0.0129400072694713,0.00409047591853073,0.0313347429139471,0.234465653537149,0.145831387105995,0.380725815830876,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,2.54918143208584,0.805823755950554,6.17294435404758,1.69305134846871,0.516197581848707,4.65492910955706,1.54918143208584,1.30694865153129,No PCV +Bogota.pre.PCV,18A,197,357200,4,1,1,adjusted_type_specific_negbin,0.00965684606346479,0.00199654764668233,0.0287128869720228,0.234465653537149,0.145831387105995,0.380725815830876,0.000199167672918468,2.36758150914551e-05,0.00102580832813065,3.54405372684984,2.48735345296771,5.1992340148223,1.90239867450256,0.393319886396419,5.65643873348848,0.61441863509029,0.0634387764544155,3.26401263469034,0.902398674502563,0.38558136490971,No PCV +Bogota.pre.PCV,18B,197,357200,4,0,1,adjusted_type_specific_negbin,0.00285285813953689,0.000281223293440886,0.0132953334856558,0.234465653537149,0.145831387105995,0.380725815830876,0.00124537383207727,0.000230254934727611,0.00649327559125252,3.54405372684984,2.48735345296771,5.1992340148223,0.562013053488768,0.0554009888078546,2.61918069667419,1.16074606180255,0.136824822681299,5.90730265857971,0.562013053488768,0.160746061802549,No PCV +Bogota.pre.PCV,18C,197,357200,4,3,11,adjusted_type_specific_negbin,0.0160267124273349,0.00636912354187998,0.0359054626661979,0.234465653537149,0.145831387105995,0.380725815830876,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,3.15726234818498,1.25471733775036,7.07337614524099,14.3645901878149,5.90297220554077,36.3520715856379,0.157262348184979,3.36459018781491,PCV7 +Bogota.pre.PCV,18F,197,357200,4,0,2,adjusted_type_specific_negbin,0.00564424617600859,0.000698219470833055,0.0212721969737586,0.234465653537149,0.145831387105995,0.380725815830876,0.000715462278901391,6.42185069257939e-05,0.00686363084750182,3.54405372684984,2.48735345296771,5.1992340148223,1.11191649667369,0.137549235754112,4.19062280383045,1.27926318366144,0.15539828525122,6.58171379355975,1.11191649667369,0.720736816338564,No PCV +Bogota.pre.PCV,19A,197,357200,4,3,10,adjusted_type_specific_negbin,0.0195333935154382,0.00843224035545922,0.0402980245047164,0.234465653537149,0.145831387105995,0.380725815830876,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,3.84807852254133,1.66115135002547,7.93871082742914,10.0607883661882,4.3929608083314,22.0692675336945,0.848078522541328,0.0607883661882287,PCV13 +Bogota.pre.PCV,19B,197,357200,4,1,0,adjusted_type_specific_negbin,0.00786441075936783,0.00112244659626166,0.0264398050049888,0.234465653537149,0.145831387105995,0.380725815830876,1.18969542866196e-05,1.13237127398798e-06,0.000461834995257341,3.54405372684984,2.48735345296771,5.1992340148223,1.54928891959546,0.221121979463547,5.2086415859828,0.030960323286641,0.00138169768037761,1.09787983806631,0.549288919595463,0.030960323286641,No PCV +Bogota.pre.PCV,19F,197,357200,4,25,13,adjusted_type_specific_negbin,0.122687180969025,0.083094869429581,0.172046406015242,0.234465653537149,0.145831387105995,0.380725815830876,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,24.1693746508979,16.3696892776275,33.8931419850028,26.1605927148311,14.4270090841958,47.995587187268,0.830625349102135,13.1605927148311,PCV7 +Bogota.pre.PCV,22F,197,357200,4,0,2,adjusted_type_specific_negbin,0.0049659487398886,0.000998662762331247,0.0164039009904864,0.234465653537149,0.145831387105995,0.380725815830876,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,0.978291901758053,0.196736564179256,3.23156849512582,1.70340336641046,0.353202185776203,5.72502118572569,0.978291901758053,0.296596633589539,PCV15 +Bogota.pre.PCV,23A,197,357200,4,5,2,adjusted_type_specific_negbin,0.0299097565746364,0.0131879816521493,0.0575733108643568,0.234465653537149,0.145831387105995,0.380725815830876,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,5.89222204520337,2.59803238547342,11.3419422402783,1.58192878528162,0.588254043308758,3.78364253720773,0.892222045203374,0.418071214718382,No PCV +Bogota.pre.PCV,23B,197,357200,4,2,1,adjusted_type_specific_negbin,0.0130996270744587,0.00372230637670832,0.0324288813155852,0.234465653537149,0.145831387105995,0.380725815830876,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,2.58062653366837,0.733294356211539,6.38848961917028,1.11652617423834,0.297440712306994,3.22147880893513,0.580626533668372,0.116526174238337,No PCV +Bogota.pre.PCV,23F,197,357200,4,7,9,adjusted_type_specific_negbin,0.0393750094076699,0.0202532756203812,0.0685887819377134,0.234465653537149,0.145831387105995,0.380725815830876,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,7.75687685331097,3.98989529721509,13.5119900417295,9.00388315845769,4.3131310124537,18.1938217846447,0.756876853310965,0.00388315845769149,PCV7 +Bogota.pre.PCV,24F,197,357200,4,0,2,adjusted_type_specific_negbin,0.00312916971533971,0.00056832468059429,0.0120740446710164,0.234465653537149,0.145831387105995,0.380725815830876,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,0.616446433921923,0.111959962077075,2.37858680019024,2.2908732903786,0.447074521090378,8.87846388350698,0.616446433921923,0.290873290378602,No PCV +Bogota.pre.PCV,25A,197,357200,4,1,2,adjusted_type_specific_negbin,0.00591208077751097,0.00127518795830209,0.0192226960205338,0.234465653537149,0.145831387105995,0.380725815830876,0.00163929978568756,0.000579341956760081,0.00489291543751703,3.54405372684984,2.48735345296771,5.1992340148223,1.16467991316966,0.251212027785511,3.78687111604516,3.15926778189591,0.766189223698387,11.3536835544828,0.164679913169662,1.15926778189591,No PCV +Bogota.pre.PCV,3,197,357200,4,1,6,adjusted_type_specific_negbin,0.00914179935470596,0.00303108461992294,0.0230808936784848,0.234465653537149,0.145831387105995,0.380725815830876,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,1.80093447287707,0.597123670124819,4.54693605466151,6.17410260312827,2.17407023865374,16.3988143681992,0.800934472877074,0.174102603128269,PCV13 +Bogota.pre.PCV,34,197,357200,4,3,0,adjusted_type_specific_negbin,0.0160604908825157,0.00465801183489511,0.0389738966388276,0.234465653537149,0.145831387105995,0.380725815830876,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,3.16391670385559,0.917628331474336,7.67785763784903,0.520692936344761,0.0849815519129644,2.16816827849467,0.163916703855594,0.520692936344761,No PCV +Bogota.pre.PCV,35C,197,357200,4,0,1,adjusted_type_specific_negbin,0.00351758006124135,0.000132259078024698,0.0186098886103753,0.234465653537149,0.145831387105995,0.380725815830876,0.000679276228433147,1.46199607572675e-05,0.0329212066103268,3.54405372684984,2.48735345296771,5.1992340148223,0.692963272064545,0.0260550383708654,3.66614805624393,0.75767286789011,0.0246151399221777,6.70689070376487,0.692963272064545,0.24232713210989,No PCV +Bogota.pre.PCV,35F,197,357200,4,2,1,adjusted_type_specific_negbin,0.0146088006856258,0.0041130229801439,0.0353767131681766,0.234465653537149,0.145831387105995,0.380725815830876,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,2.87793373506829,0.810265527088349,6.9692124941308,0.718385831001499,0.178856785389192,2.21772720968037,0.877933735068293,0.281614168998501,No PCV +Bogota.pre.PCV,4,197,357200,4,2,5,adjusted_type_specific_negbin,0.0110484276224624,0.00373460634621018,0.0277405357632588,0.234465653537149,0.145831387105995,0.380725815830876,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,2.17654024162509,0.735717450203405,5.46488554536197,6.98103821299119,2.41390820651301,19.286662311439,0.176540241625088,1.98103821299119,PCV7 +Bogota.pre.PCV,5,197,357200,4,0,5,adjusted_type_specific_negbin,0.00255701960815108,0.000570086164448778,0.00999791913613391,0.234465653537149,0.145831387105995,0.380725815830876,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,0.503732862805763,0.112306974396409,1.96959006981838,6.16629918794804,1.74568356127314,22.2854822043008,0.503732862805763,1.16629918794804,PCV10 +Bogota.pre.PCV,6A,197,357200,4,23,16,adjusted_type_specific_negbin,0.119082434761421,0.0803032476957868,0.167312962966365,0.234465653537149,0.145831387105995,0.380725815830876,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,23.459239648,15.81973979607,32.9606537043739,17.1980394499941,9.66270895548648,30.8326745228922,0.459239647999958,1.19803944999412,PCV13 +Bogota.pre.PCV,6B,197,357200,4,12,26,adjusted_type_specific_negbin,0.0710726633782921,0.0437349009784695,0.108852314546168,0.234465653537149,0.145831387105995,0.380725815830876,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,14.0013146855235,8.6157754927585,21.4439059655951,17.6828742013692,9.80089067651432,32.1697475532618,2.00131468552355,8.31712579863076,PCV7 +Bogota.pre.PCV,7C,197,357200,4,0,1,adjusted_type_specific_negbin,0.00488981140476359,0.00064719455899815,0.0181855569044109,0.234465653537149,0.145831387105995,0.380725815830876,0.000393012283852677,0.00011306744230165,0.00121318243232636,3.54405372684984,2.48735345296771,5.1992340148223,0.963292846738427,0.127497328122635,3.58255471016895,0.631375398034866,0.0754372641925484,2.89259497407068,0.963292846738427,0.368624601965134,No PCV +Bogota.pre.PCV,7F,197,357200,4,0,3,adjusted_type_specific_negbin,0.00143194746515712,0.000279635931658409,0.00669203374019089,0.234465653537149,0.145831387105995,0.380725815830876,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,0.282093650635954,0.0550882785367065,1.31833064681761,4.51957192594311,0.985402919887066,20.1518806645811,0.282093650635954,1.51957192594311,PCV10 +Bogota.pre.PCV,8,197,357200,4,0,1,adjusted_type_specific_negbin,0.00229520260944028,0.000274644920386549,0.0103627677724433,0.234465653537149,0.145831387105995,0.380725815830876,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,0.452154914059735,0.0541050493161501,2.04146525117134,1.45874691002487,0.188603183020647,6.57578842447666,0.452154914059735,0.458746910024868,PCV20 +Bogota.pre.PCV,9N,197,357200,4,5,2,adjusted_type_specific_negbin,0.0240846315857478,0.00985229287444615,0.0489014312759318,0.234465653537149,0.145831387105995,0.380725815830876,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,4.74467242239233,1.94090169626589,9.63358196135856,4.14054548727552,1.42859266095377,11.287430790657,0.255327577607673,2.14054548727552,PPV23 +Bogota.pre.PCV,9V,197,357200,4,0,8,adjusted_type_specific_negbin,0.00855333840747477,0.00286177011784186,0.0219575093800765,0.234465653537149,0.145831387105995,0.380725815830876,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,1.68500766627253,0.563768713214847,4.32562934787508,5.80402783251185,2.12855004867396,15.1770284094487,1.68500766627253,2.19597216748815,PCV7 +Caracas.pre.PCV,1,1004,146125,1,0,2,adjusted_type_specific_negbin,0.000842017638470613,0.000157509542556088,0.00291319515655589,0.911094123892749,0.463708955849939,1.80193463046918,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,0.845385709024495,0.158139580726313,2.92484793718211,1.91523603514396,0.383568748465079,6.81693737582375,0.845385709024495,0.0847639648560423,PCV10 +Caracas.pre.PCV,14,1004,146125,1,23,6,adjusted_type_specific_negbin,0.0222396181120387,0.0144566125615658,0.0325912241200537,0.911094123892749,0.463708955849939,1.80193463046918,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,22.3285765844869,14.5144390118121,32.7215890165339,12.4830065180243,5.95468073495486,26.7974289219453,0.671423415513132,6.48300651802434,PCV7 +Caracas.pre.PCV,19A,1004,146125,1,32,3,adjusted_type_specific_negbin,0.0313726423576946,0.0219616191870564,0.0430167537719332,0.911094123892749,0.463708955849939,1.80193463046918,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,31.4981329271254,22.0494656638046,43.1888207870209,6.42745573146209,3.18690589449076,13.2768374879171,0.501867072874632,3.42745573146209,PCV13 +Caracas.pre.PCV,19F,1004,146125,1,3,2,adjusted_type_specific_negbin,0.00501706951742916,0.00193969694379345,0.0104392010917587,0.911094123892749,0.463708955849939,1.80193463046918,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,5.03713779549888,1.94745573156862,10.4809578961257,0.424111246126028,0.139770915703875,1.13082182405991,2.03713779549888,1.57588875387397,PCV7 +Caracas.pre.PCV,23F,1004,146125,1,25,1,adjusted_type_specific_negbin,0.0247860153394341,0.0165714362087811,0.035504187044229,0.911094123892749,0.463708955849939,1.80193463046918,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,24.8851594007918,16.6377219536162,35.6462037924059,2.2573247253483,1.05893611129342,4.90942003306794,0.114840599208165,1.2573247253483,PCV7 +Caracas.pre.PCV,3,1004,146125,1,2,1,adjusted_type_specific_negbin,0.00283120444274258,0.00081070764301375,0.00704498725836204,0.911094123892749,0.463708955849939,1.80193463046918,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,2.84252926051355,0.813950473585805,7.07316720739549,0.761227494344744,0.197941514790228,2.26125736752501,0.842529260513554,0.238772505655256,PCV13 +Caracas.pre.PCV,4,1004,146125,1,3,0,adjusted_type_specific_negbin,0.00301024933065842,0.000847809867974719,0.00749428093947953,0.911094123892749,0.463708955849939,1.80193463046918,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,3.02229032798105,0.851201107446618,7.52425806323744,0.759558680924262,0.187512172144979,2.43726634912183,0.0222903279810494,0.759558680924262,PCV7 +Caracas.pre.PCV,5,1004,146125,1,0,2,adjusted_type_specific_negbin,0.00125823720846078,0.000248789967980229,0.00396179298299755,0.911094123892749,0.463708955849939,1.80193463046918,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,1.26327015729462,0.24978512785215,3.97764015492954,1.22105409873104,0.248016647102813,4.39557177119716,1.26327015729462,0.77894590126896,PCV10 +Caracas.pre.PCV,6A,1004,146125,1,20,3,adjusted_type_specific_negbin,0.0218705604375327,0.0142854976602432,0.0317242160515295,0.911094123892749,0.463708955849939,1.80193463046918,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,21.9580426792828,14.3426396508842,31.8511129157356,1.25596378380864,0.575886432827609,2.70309696637648,1.9580426792828,1.74403621619136,PCV13 +Caracas.pre.PCV,6B,1004,146125,1,70,10,adjusted_type_specific_negbin,0.0712458966364299,0.0563951257104467,0.0881296110769146,0.911094123892749,0.463708955849939,1.80193463046918,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,71.5308802229756,56.6207062132885,88.4821295212223,7.0746017825694,3.72001979503339,13.7522857785545,1.5308802229756,2.9253982174306,PCV7 +Caracas.pre.PCV,7F,1004,146125,1,1,3,adjusted_type_specific_negbin,0.00203254451403971,0.000586671482368418,0.00527633465679299,0.911094123892749,0.463708955849939,1.80193463046918,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,2.04067469209587,0.589018168297892,5.29743999542017,2.52125716677723,0.742877159913484,7.360837532511,1.04067469209587,0.47874283322277,PCV10 +Caracas.pre.PCV,9V,1004,146125,1,2,0,adjusted_type_specific_negbin,0.00215430129756056,0.000496554163909517,0.00602642128950942,0.911094123892749,0.463708955849939,1.80193463046918,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,2.1629185027508,0.498540380565155,6.05052697466746,0.57984456849089,0.119055559238617,2.00038361474094,0.1629185027508,0.57984456849089,PCV7 +Czech.pre.PCV,1,425,478177,9,0,9,adjusted_type_specific_negbin,0.00165756719383442,0.000479989172826237,0.00533840257113592,0.0843408445283054,0.051097182715231,0.14077921976402,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,0.704466057379627,0.203995398451151,2.26882109273276,10.2798695235926,3.44812811722981,32.4089595247881,0.704466057379627,1.27986952359263,PCV10 +Czech.pre.PCV,10A,425,478177,9,6,4,adjusted_type_specific_negbin,0.0157017798692881,0.00751311976528753,0.0290744610439626,0.0843408445283054,0.051097182715231,0.14077921976402,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,6.67325644444744,3.1930759002472,12.3566459436841,4.05009028533849,1.76261384167567,9.05036971952237,0.673256444447444,0.0500902853384861,PCV20 +Czech.pre.PCV,11A,425,478177,9,8,1,adjusted_type_specific_negbin,0.0212942547622039,0.0104750281805535,0.037766551892684,0.0843408445283054,0.051097182715231,0.14077921976402,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,9.05005827393668,4.45188697673522,16.0507845543907,0.512911816021193,0.183229212603232,1.27977495860562,1.05005827393668,0.487088183978807,PCV20 +Czech.pre.PCV,12F,425,478177,9,0,1,adjusted_type_specific_negbin,0.000776292045502717,8.86289505026334e-05,0.00380401599617523,0.0843408445283054,0.051097182715231,0.14077921976402,0.00604172772796168,0.00276457252642332,0.013992691352501,3.54405372684984,2.48735345296771,5.1992340148223,0.329924119338655,0.0376673039636192,1.61670679837447,1.69856682412676,0.219942619869263,8.2542998856121,0.329924119338655,0.698566824126763,PCV20 +Czech.pre.PCV,14,425,478177,9,5,19,adjusted_type_specific_negbin,0.0133024256672357,0.00642647462299924,0.0252340456811325,0.0843408445283054,0.051097182715231,0.14077921976402,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,5.65353090857518,2.73125171477468,10.7244694144813,20.2027468625279,9.59659065750559,43.1974422447887,0.653530908575179,1.20274686252795,PCV7 +Czech.pre.PCV,15B/C,425,478177,9,17,0,adjusted_type_specific_negbin,0.0368737135062767,0.0221972407311467,0.0570176100394056,0.0843408445283054,0.051097182715231,0.14077921976402,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,15.6713282401676,9.43382731073735,24.2324842667474,4.64867398263248,2.20897356231874,9.47883386690618,1.3286717598324,4.64867398263248,PCV20 +Czech.pre.PCV,17F,425,478177,9,0,1,adjusted_type_specific_negbin,0.00282486594130204,0.000412570462837701,0.0101491220962441,0.0843408445283054,0.051097182715231,0.14077921976402,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,1.20056802505337,0.175342446706023,4.31337689090374,0.387629240389591,0.0527715085633177,1.61871158452041,1.20056802505337,0.612370759610409,PPV23 +Czech.pre.PCV,18C,425,478177,9,9,9,adjusted_type_specific_negbin,0.0193410664888673,0.00979734323678902,0.0340967069523135,0.0843408445283054,0.051097182715231,0.14077921976402,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,8.21995325776859,4.16387087563534,14.4911004547333,18.822733245912,8.35065570576845,42.9660612859987,0.780046742231409,9.82273324591202,PCV7 +Czech.pre.PCV,19A,425,478177,9,0,2,adjusted_type_specific_negbin,0.00261395472062322,0.000570872967655312,0.00818614595680967,0.0843408445283054,0.051097182715231,0.14077921976402,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,1.11093075626487,0.242621011253508,3.47911203164411,1.46096383758757,0.321747242811373,4.76892847514359,1.11093075626487,0.539036162412429,PCV13 +Czech.pre.PCV,19F,425,478177,9,10,12,adjusted_type_specific_negbin,0.0293255539921958,0.0171868998482741,0.0461879992711846,0.0843408445283054,0.051097182715231,0.14077921976402,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,12.4633604466832,7.30443243551649,19.6298996902535,6.77799936722495,3.59282725237554,12.8112466702217,2.4633604466832,5.22200063277505,PCV7 +Czech.pre.PCV,23A,425,478177,9,3,1,adjusted_type_specific_negbin,0.00948078393123135,0.00328808350237115,0.0209840360625925,0.0843408445283054,0.051097182715231,0.14077921976402,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,4.02933317077332,1.39743548850774,8.91821532660183,0.541573676739421,0.160055686391479,1.52487026841409,1.02933317077332,0.458426323260579,No PCV +Czech.pre.PCV,23F,425,478177,9,30,13,adjusted_type_specific_negbin,0.0704127803067444,0.049734797609088,0.0959783553665698,0.0843408445283054,0.051097182715231,0.14077921976402,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,29.9254316303664,21.1372889838624,40.7908010307922,17.4722524093751,9.71272208691485,32.6596978555137,0.0745683696336172,4.47225240937508,PCV7 +Czech.pre.PCV,28F,425,478177,9,0,2,adjusted_type_specific_negbin,0.0036341909587752,0.000612946124274606,0.0117998440971713,0.0843408445283054,0.051097182715231,0.14077921976402,0.000617113246724779,6.12527157324586e-05,0.00520565109745502,3.54405372684984,2.48735345296771,5.1992340148223,1.54453115747946,0.260502102816707,5.01493374129781,0.789590495587569,0.0831127796321062,4.44529631034418,1.54453115747946,1.21040950441243,No PCV +Czech.pre.PCV,3,425,478177,9,6,5,adjusted_type_specific_negbin,0.0130227282476397,0.00600018103108643,0.0255078579889718,0.0843408445283054,0.051097182715231,0.14077921976402,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,5.53465950524686,2.55007693821173,10.840839645313,9.54368937189191,4.03301196892678,21.9585195151551,0.465340494753145,4.54368937189191,PCV13 +Czech.pre.PCV,33F,425,478177,9,0,1,adjusted_type_specific_negbin,0.0018593015690979,0.000252191020547659,0.00707400024665856,0.0843408445283054,0.051097182715231,0.14077921976402,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,0.790203166866607,0.107181183732755,3.00645010482989,0.893706192439893,0.122471203971437,3.62166268694223,0.790203166866607,0.106293807560107,PCV15 +Czech.pre.PCV,35F,425,478177,9,5,0,adjusted_type_specific_negbin,0.011970435276514,0.00459701581173683,0.0247881668577916,0.0843408445283054,0.051097182715231,0.14077921976402,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,5.08743499251843,1.95373171998815,10.5349709145614,0.636645413936104,0.193818042681385,1.86291198599267,0.0874349925184319,0.636645413936104,No PCV +Czech.pre.PCV,37,425,478177,9,2,1,adjusted_type_specific_negbin,0.00768023882210329,0.00224381531305512,0.0187665025255735,0.0843408445283054,0.051097182715231,0.14077921976402,8.82466692072548e-05,4.22185054013693e-06,0.000564483172719643,3.54405372684984,2.48735345296771,5.1992340148223,3.2641014993939,0.953621508048427,7.97576357336872,0.236887012758761,0.0110171459688595,1.5924600949331,1.2641014993939,0.763112987241239,No PCV +Czech.pre.PCV,38,425,478177,9,1,1,adjusted_type_specific_negbin,0.00366823805999817,0.000775793052045025,0.0112268938011733,0.0843408445283054,0.051097182715231,0.14077921976402,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,1.55900117549922,0.329712047119136,4.77142986549863,1.15569945327379,0.231489264668283,4.10986203485845,0.55900117549922,0.15569945327379,No PCV +Czech.pre.PCV,4,425,478177,9,2,5,adjusted_type_specific_negbin,0.00685714095647201,0.00252200474298912,0.0156926448502574,0.0843408445283054,0.051097182715231,0.14077921976402,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,2.9142849065006,1.07185201577038,6.66937406135941,4.68841930705881,1.71382223827745,11.948561802763,0.914284906500605,0.311580692941188,PCV7 +Czech.pre.PCV,40,425,478177,9,0,1,adjusted_type_specific_negbin,0.00163590930646822,5.51621156701614e-05,0.00872855465561547,0.0843408445283054,0.051097182715231,0.14077921976402,0.00135916598823838,2.93565010093865e-05,0.0683656889341698,3.54405372684984,2.48735345296771,5.1992340148223,0.695261455248992,0.0234438991598186,3.70963572863658,0.771156619873487,0.0259507802801461,6.62884168368051,0.695261455248992,0.228843380126513,No PCV +Czech.pre.PCV,5,425,478177,9,0,1,adjusted_type_specific_negbin,0.000668658303871552,6.96561427860758e-05,0.00353862720934006,0.0843408445283054,0.051097182715231,0.14077921976402,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,0.28417977914541,0.0296038606840822,1.50391656396953,1.77591561445374,0.208206526808193,9.09467812111167,0.28417977914541,0.775915614453739,PCV10 +Czech.pre.PCV,6A,425,478177,9,24,8,adjusted_type_specific_negbin,0.0573431283373731,0.0385211692440123,0.0815634873568264,0.0843408445283054,0.051097182715231,0.14077921976402,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,24.3708295433836,16.3714969287052,34.6644821266512,8.96282647385986,4.88464931770953,16.7782190871726,0.37082954338355,0.962826473859863,PCV13 +Czech.pre.PCV,6B,425,478177,9,21,23,adjusted_type_specific_negbin,0.0546761577570314,0.0369391475084355,0.077150824736276,0.0843408445283054,0.051097182715231,0.14077921976402,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,23.2373670467383,15.6991376910851,32.7891005129173,14.7290046588897,8.43648903616611,26.2141146915378,2.23736704673833,8.27099534111026,PCV7 +Czech.pre.PCV,7F,425,478177,9,1,6,adjusted_type_specific_negbin,0.00261493305417426,0.000771959667129526,0.00776443852686901,0.0843408445283054,0.051097182715231,0.14077921976402,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,1.11134654802406,0.328082858530049,3.29988637391933,8.92414801226422,2.88356795302456,27.4785312788089,0.111346548024059,2.92414801226422,PCV10 +Czech.pre.PCV,8,425,478177,9,1,1,adjusted_type_specific_negbin,0.00272974381013096,0.000551607515285856,0.00904337830806914,0.0843408445283054,0.051097182715231,0.14077921976402,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,1.16014111930566,0.234433193996489,3.84343578092939,1.87395174106205,0.384673354326249,6.85155755372306,0.160141119305658,0.873951741062045,PCV20 +Czech.pre.PCV,9N,425,478177,9,1,2,adjusted_type_specific_negbin,0.00562541747846894,0.00152783107771453,0.0144793804670345,0.0843408445283054,0.051097182715231,0.14077921976402,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,2.3908024283493,0.649328208028674,6.15373669848967,1.04856408201524,0.26063047597546,3.3294505296442,1.3908024283493,0.951435917984761,PPV23 +Czech.pre.PCV,9V,425,478177,9,1,9,adjusted_type_specific_negbin,0.00745567039601635,0.00296871544705203,0.0163940645213266,0.0843408445283054,0.051097182715231,0.14077921976402,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,3.16865991830695,1.26170406499711,6.96747742156382,5.49692554950219,2.22548197476765,12.9562557164567,2.16865991830695,3.50307445049781,PCV7 +France.post.PCV7,1,1212,838866,2,2,30,adjusted_type_specific_negbin,0.00140785429130437,0.000491950062985152,0.00375333617697367,1.21249730072015,0.78870178835535,1.88425821404601,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,1.70631940106089,0.596243476338004,4.54904344649209,48.9688093150699,18.5899019574652,138.390548498993,0.29368059893911,18.9688093150699,PCV10 +France.post.PCV7,10A,1212,838866,2,0,7,adjusted_type_specific_negbin,0.00224259878098859,0.000844561091431066,0.00507567662072453,1.21249730072015,0.78870178835535,1.88425821404601,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,2.71802972255817,1.02360804281445,6.15172006431813,3.26885957701674,1.24988684976931,7.66725677758625,2.71802972255817,3.73114042298326,PCV20 +France.post.PCV7,10B,1212,838866,2,0,1,adjusted_type_specific_negbin,0.00071356422880494,8.63176647376274e-05,0.0028809091056433,1.21249730072015,0.78870178835535,1.88425821404601,0.000502204985915827,8.47222594103277e-05,0.00253825696624574,3.54405372684984,2.48735345296771,5.1992340148223,0.864839845311588,0.104617009662004,3.49166183603968,0.709795339733561,0.076479682021401,3.75486721274832,0.864839845311588,0.290204660266439,No PCV +France.post.PCV7,11A,1212,838866,2,10,1,adjusted_type_specific_negbin,0.00868418466385448,0.00459063909042628,0.0147495047992563,1.21249730072015,0.78870178835535,1.88425821404601,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,10.5252318125916,5.56385457759666,17.8763998166987,1.17387328950383,0.458953667597712,2.74220629966415,0.525231812591629,0.173873289503833,PCV20 +France.post.PCV7,12B,1212,838866,2,1,1,adjusted_type_specific_negbin,0.00100276977926314,0.000143843170843267,0.00373869723091751,1.21249730072015,0.78870178835535,1.88425821404601,0.000803657589123718,7.15519052189715e-05,0.00720297300827742,3.54405372684984,2.48735345296771,5.1992340148223,1.21535697246693,0.174337923062039,4.53130104387202,1.55352531916538,0.179509705268376,8.74810797694938,0.215356972466929,0.55352531916538,No PCV +France.post.PCV7,12F,1212,838866,2,0,9,adjusted_type_specific_negbin,0.000753889467627198,0.000212275419394314,0.00236673983100566,1.21249730072015,0.78870178835535,1.88425821404601,0.00604172772796168,0.00276457252642332,0.013992691352501,3.54405372684984,2.48735345296771,5.1992340148223,0.913714034764164,0.257277808305908,2.86848867517886,9.19388849434446,3.15376228263595,27.7238272710708,0.913714034764164,0.193888494344463,PCV20 +France.post.PCV7,14,1212,838866,2,0,6,adjusted_type_specific_negbin,0.000717780943825026,0.000215367827986332,0.00218307187044351,1.21249730072015,0.78870178835535,1.88425821404601,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,0.869950503915932,0.261025807519435,2.64588310697753,6.177586719108,1.99156518082421,18.4389709883874,0.869950503915932,0.177586719108003,PCV7 +France.post.PCV7,15A,1212,838866,2,13,6,adjusted_type_specific_negbin,0.0106486473704559,0.00614628097891408,0.0171443405401884,1.21249730072015,0.78870178835535,1.88425821404601,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,12.9061606129925,7.44929254644387,20.7789407347083,8.94580414357595,4.24847472939269,18.8873540020769,0.0938393870074954,2.94580414357595,No PCV +France.post.PCV7,15B/C,1212,838866,2,23,17,adjusted_type_specific_negbin,0.0200637290413701,0.013455117053123,0.0286235185966855,1.21249730072015,0.78870178835535,1.88425821404601,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,24.3172395981405,16.307601868385,34.6917045391828,14.2134345253574,8.04975288126192,25.4466725090632,1.31723959814052,2.78656547464264,PCV20 +France.post.PCV7,15F,1212,838866,2,1,0,adjusted_type_specific_negbin,0.00105488580657464,0.000140426845997005,0.00380386559650808,1.21249730072015,0.78870178835535,1.88425821404601,0.000169416469056684,1.99360904401105e-05,0.000839805104163891,3.54405372684984,2.48735345296771,5.1992340148223,1.27852159756846,0.17019733734837,4.6102851029678,0.346395809601278,0.0249886784164174,2.21471147800794,0.278521597568459,0.346395809601278,No PCV +France.post.PCV7,16F,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000812018439306313,0.000105326611959675,0.00293965225507197,1.21249730072015,0.78870178835535,1.88425821404601,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,0.984166348439252,0.127655853695126,3.56285853314722,0.648158943769636,0.0840445612755862,2.58333831523803,0.984166348439252,0.351841056230364,No PCV +France.post.PCV7,17F,1212,838866,2,4,4,adjusted_type_specific_negbin,0.00421051814939144,0.00182428794957047,0.00845355199426004,1.21249730072015,0.78870178835535,1.88425821404601,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,5.10314799706243,2.2110369948794,10.2457050170432,3.24466684011431,1.22461848323326,8.00357116336078,1.10314799706243,0.755333159885686,PPV23 +France.post.PCV7,18A,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000963145130124454,0.000124839889582368,0.00353434573284317,1.21249730072015,0.78870178835535,1.88425821404601,0.000199167672918468,2.36758150914551e-05,0.00102580832813065,3.54405372684984,2.48735345296771,5.1992340148223,1.16733189771084,0.15130594617383,4.28362702820592,0.367152472402766,0.0292924737340203,2.19712697680533,1.16733189771084,0.632847527597234,No PCV +France.post.PCV7,18C,1212,838866,2,0,2,adjusted_type_specific_negbin,0.000457251161572552,8.43814468758234e-05,0.00171702062388695,1.21249730072015,0.78870178835535,1.88425821404601,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,0.554188407825933,0.102270313613498,2.08102899615098,2.52324004761409,0.49329238046108,9.41337019484261,0.554188407825933,0.523240047614093,PCV7 +France.post.PCV7,19A,1212,838866,2,28,128,adjusted_type_specific_negbin,0.0253598647767442,0.0180986193292667,0.0347224242934773,1.21249730072015,0.78870178835535,1.88425821404601,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,30.736156109414,21.9355266270712,42.0835782436945,79.6358537685189,49.6475729653303,129.749944580981,2.73615610941402,48.3641462314811,PCV13 +France.post.PCV7,19F,1212,838866,2,8,10,adjusted_type_specific_negbin,0.00733598961904757,0.00392797918373675,0.012637011154099,1.21249730072015,0.78870178835535,1.88425821404601,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,8.89121941828566,4.76071077068894,15.316057518768,9.54053101755305,4.80678845356519,18.5634421697305,0.891219418285658,0.459468982446946,PCV7 +France.post.PCV7,20,1212,838866,2,1,0,adjusted_type_specific_negbin,0.000714191454889004,9.23175552181646e-05,0.00285027758431377,1.21249730072015,0.78870178835535,1.88425821404601,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,0.865600043325473,0.111888876924416,3.45453643218829,1.09192416802687,0.135903867376315,5.31907943065395,0.134399956674527,1.09192416802687,PPV23 +France.post.PCV7,21,1212,838866,2,11,3,adjusted_type_specific_negbin,0.00933841849804439,0.00514208212174634,0.0155746786105673,1.21249730072015,0.78870178835535,1.88425821404601,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,11.3181632196298,6.23220353155656,18.8765104760075,3.76976850109038,1.53165112606166,8.83926649903476,0.318163219629799,0.769768501090375,No PCV +France.post.PCV7,22F,1212,838866,2,3,6,adjusted_type_specific_negbin,0.00304245168332059,0.00124045285306732,0.00647511358463698,1.21249730072015,0.78870178835535,1.88425821404601,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,3.68745144018455,1.5034288579176,7.84783766458002,6.28348203172552,2.54342385701546,14.7777192667523,0.68745144018455,0.283482031725521,PCV15 +France.post.PCV7,23A,1212,838866,2,8,2,adjusted_type_specific_negbin,0.00702776675984784,0.00348273417964241,0.0124845034943685,1.21249730072015,0.78870178835535,1.88425821404601,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,8.51765331293558,4.2210738257266,15.1312182351747,2.25726890408747,0.921149495115233,5.13556883584348,0.517653312935575,0.257268904087475,No PCV +France.post.PCV7,23B,1212,838866,2,10,3,adjusted_type_specific_negbin,0.00833198384224359,0.00444576863835992,0.0141199612706498,1.21249730072015,0.78870178835535,1.88425821404601,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,10.0983644167992,5.38827158969222,17.1133930600276,4.33080965725242,1.95128570984002,9.41229943589073,0.0983644167992264,1.33080965725242,No PCV +France.post.PCV7,23F,1212,838866,2,3,2,adjusted_type_specific_negbin,0.00250024785888402,0.000875123129298099,0.00584649970297365,1.21249730072015,0.78870178835535,1.88425821404601,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,3.03030040496743,1.0606492327093,7.08595764000406,3.46661359917669,1.18247000739837,8.86698845778752,0.0303004049674263,1.46661359917669,PCV7 +France.post.PCV7,24B,1212,838866,2,0,3,adjusted_type_specific_negbin,0.000494543977010725,3.99677535415997e-05,0.00248803342504683,1.21249730072015,0.78870178835535,1.88425821404601,0.00349173287124971,0.000414261332271996,0.0415103510785451,3.54405372684984,2.48735345296771,5.1992340148223,0.599387300136998,0.0484409172924189,3.01549651115676,3.27258303414655,0.700925113758359,15.0310712499362,0.599387300136998,0.272583034146554,No PCV +France.post.PCV7,24F,1212,838866,2,2,25,adjusted_type_specific_negbin,0.00367787646386059,0.0016507756789392,0.00737756025349989,1.21249730072015,0.78870178835535,1.88425821404601,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,4.45758627419903,2.00074012287431,8.94160302724187,16.1802524837038,7.64768260058526,34.9710729040957,2.45758627419903,8.81974751629623,No PCV +France.post.PCV7,25A,1212,838866,2,0,15,adjusted_type_specific_negbin,0.0024653149444238,0.000864706264544459,0.00572064277010785,1.21249730072015,0.78870178835535,1.88425821404601,0.00163929978568756,0.000579341956760081,0.00489291543751703,3.54405372684984,2.48735345296771,5.1992340148223,2.98796171264164,1.04802399262788,6.93341903737072,8.02160947960222,3.4130143079322,19.7463538766098,2.98796171264164,6.97839052039778,No PCV +France.post.PCV7,28F,1212,838866,2,1,0,adjusted_type_specific_negbin,0.000736148485949916,7.98016381574222e-05,0.00313425183894695,1.21249730072015,0.78870178835535,1.88425821404601,0.000617113246724779,6.12527157324586e-05,0.00520565109745502,3.54405372684984,2.48735345296771,5.1992340148223,0.892211964971298,0.0967195854467957,3.79871322880371,0.882938113885754,0.0720299083539895,6.1805767744032,0.107788035028702,0.882938113885754,No PCV +France.post.PCV7,29,1212,838866,2,3,0,adjusted_type_specific_negbin,0.00267138710134838,0.000768911837095122,0.00654803176854047,1.21249730072015,0.78870178835535,1.88425821404601,6.4477890005963e-05,3.10034323663527e-06,0.000486340435351969,3.54405372684984,2.48735345296771,5.1992340148223,3.23772116683424,0.931921146559288,7.93621450347105,0.339230440675968,0.0159400034419865,2.60883627513294,0.237721166834238,0.339230440675968,No PCV +France.post.PCV7,3,1212,838866,2,1,18,adjusted_type_specific_negbin,0.00282453914666239,0.00124517835740535,0.00581787798823141,1.21249730072015,0.78870178835535,1.88425821404601,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,3.42334144575482,1.50915616917528,7.05126812173647,11.5789631718104,5.39294178274594,24.823302203118,2.42334144575482,6.42103682818957,PCV13 +France.post.PCV7,31,1212,838866,2,0,2,adjusted_type_specific_negbin,0.00112663806223986,0.000238271312513902,0.00351938484291845,1.21249730072015,0.78870178835535,1.88425821404601,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,1.36548533143471,0.28878483076685,4.26549442961717,1.09236057132412,0.219960422100981,3.93601506080262,1.36548533143471,0.907639428675877,No PCV +France.post.PCV7,33F,1212,838866,2,3,5,adjusted_type_specific_negbin,0.00259267548191864,0.000972682221794295,0.0059236650003152,1.21249730072015,0.78870178835535,1.88425821404601,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,3.14232268408539,1.17889085281469,7.17948198038203,6.94837247909229,2.63751705582781,18.0111014968316,0.142322684085393,1.94837247909229,PCV15 +France.post.PCV7,34,1212,838866,2,1,0,adjusted_type_specific_negbin,0.00118607431493992,0.000176227424536971,0.00395981649123617,1.21249730072015,0.78870178835535,1.88425821404601,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,1.43752206970719,0.213587638538809,4.79929758737824,0.231694996986361,0.0231363419452987,1.21357186923804,0.437522069707187,0.231694996986361,No PCV +France.post.PCV7,35B,1212,838866,2,8,1,adjusted_type_specific_negbin,0.00670268724963093,0.00321910312801203,0.0121474675396537,1.21249730072015,0.78870178835535,1.88425821404601,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,8.12365694655269,3.90155299115058,14.7227306580603,1.76213079427124,0.63087727842839,4.46409730366454,0.123656946552689,0.762130794271243,No PCV +France.post.PCV7,35F,1212,838866,2,7,3,adjusted_type_specific_negbin,0.00681166537068905,0.00337196262105439,0.0121470612211238,1.21249730072015,0.78870178835535,1.88425821404601,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,8.25573842927513,4.08681869671792,14.7222382000021,2.05100783135313,0.770708444512207,4.97193914325975,1.25573842927513,0.94899216864687,No PCV +France.post.PCV7,4,1212,838866,2,2,0,adjusted_type_specific_negbin,0.000879877346399739,0.000167915301352387,0.00307105049860779,1.21249730072015,0.78870178835535,1.88425821404601,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,1.06641134383648,0.203513345239093,3.72211320431264,3.35924196147078,0.662178986615899,12.9828387150198,0.933588656163516,3.35924196147078,PCV7 +France.post.PCV7,45,1212,838866,2,1,0,adjusted_type_specific_negbin,0.00125781635609734,0.000169768548385478,0.00433658943534595,1.21249730072015,0.78870178835535,1.88425821404601,1.59311396867691e-05,1.1560837920513e-06,0.000873937490688985,3.54405372684984,2.48735345296771,5.1992340148223,1.52447342358998,0.205759480643199,5.25594639563929,0.040821393703385,0.00149961785603541,1.67405825330387,0.52447342358998,0.040821393703385,No PCV +France.post.PCV7,46,1212,838866,2,0,1,adjusted_type_specific_negbin,2.79109431422658e-05,9.84344560134964e-07,0.000429578599291151,1.21249730072015,0.78870178835535,1.88425821404601,0.0444406031297313,0.00432635280035329,0.569810674714261,3.54405372684984,2.48735345296771,5.1992340148223,0.0338280630884261,0.00119302560688358,0.520649262340875,2.50287722628889,0.272274461416539,16.7719257878327,0.0338280630884261,1.50287722628889,No PCV +France.post.PCV7,5,1212,838866,2,0,4,adjusted_type_specific_negbin,0.000357192232571458,7.43303919070683e-05,0.00147109764388887,1.21249730072015,0.78870178835535,1.88425821404601,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,0.432916985876607,0.0900884349913668,1.78297034439331,5.22500281104874,1.36019121797135,20.5599829847431,0.432916985876607,1.22500281104874,PCV10 +France.post.PCV7,6A,1212,838866,2,10,3,adjusted_type_specific_negbin,0.00776593762154702,0.00404322828757919,0.0134404414659242,1.21249730072015,0.78870178835535,1.88425821404601,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,9.41231639731499,4.90039268454598,16.2898150567001,6.79517283304306,3.21381366695919,13.9294767625209,0.587683602685008,3.79517283304306,PCV13 +France.post.PCV7,6B,1212,838866,2,3,4,adjusted_type_specific_negbin,0.00293905700255472,0.00115956311436149,0.00638816476256739,1.21249730072015,0.78870178835535,1.88425821404601,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,3.56213708709632,1.40539049460612,7.74245569223168,4.45378399698342,1.71666932192906,10.4326666006773,0.562137087096324,0.453783996983418,PCV7 +France.post.PCV7,6C,1212,838866,2,13,4,adjusted_type_specific_negbin,0.01224296380239,0.00717069094946911,0.0193738086147732,1.21249730072015,0.78870178835535,1.88425821404601,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,14.8384721284967,8.69087743075656,23.4810560411051,2.06180402547292,0.802400425409961,4.89356112258542,1.83847212849669,1.93819597452708,No PCV +France.post.PCV7,7C,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000808760561270143,0.000108011484621145,0.00302105602516998,1.21249730072015,0.78870178835535,1.88425821404601,0.000393012283852677,0.00011306744230165,0.00121318243232636,3.54405372684984,2.48735345296771,5.1992340148223,0.980217800259413,0.130909919360828,3.66151990250601,0.627561856917938,0.0778666863012016,2.91116071784028,0.980217800259413,0.372438143082062,No PCV +France.post.PCV7,7F,1212,838866,2,2,53,adjusted_type_specific_negbin,0.0026270869164513,0.00114246704054578,0.00556973738100661,1.21249730072015,0.78870178835535,1.88425821404601,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,3.18402934273897,1.38467005314148,6.75052170578001,50.1517191594832,23.2570505096089,114.050023716081,1.18402934273897,2.8482808405168,PCV10 +France.post.PCV7,8,1212,838866,2,1,1,adjusted_type_specific_negbin,0.000694654951128483,0.000130162744844802,0.0025105804019892,1.21249730072015,0.78870178835535,1.88425821404601,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,0.841921800767721,0.1577572467519,3.04282344721091,2.67493247130543,0.543337093972737,10.3870884925474,0.158078199232279,1.67493247130543,PCV20 +France.post.PCV7,9A,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000797919094920828,7.99619674523824e-05,0.00331201250645504,1.21249730072015,0.78870178835535,1.88425821404601,0.000322376410083512,8.54282288459075e-06,0.00437510447699665,3.54405372684984,2.48735345296771,5.1992340148223,0.967077943044043,0.0969139045522875,4.01415915782351,0.49163700801717,0.0156246333182224,3.95359687202788,0.967077943044043,0.50836299198283,No PCV +France.post.PCV7,9L,1212,838866,2,0,1,adjusted_type_specific_negbin,0.000289751137013091,1.52836317600924e-05,0.00199824614071203,1.21249730072015,0.78870178835535,1.88425821404601,0.00260956502335847,0.000181022012236223,0.0383407530403242,3.54405372684984,2.48735345296771,5.1992340148223,0.351178378059867,0.018523761693232,2.42187432254298,1.42649238154802,0.139363280164466,9.00220701039551,0.351178378059867,0.426492381548024,No PCV +France.post.PCV7,9N,1212,838866,2,1,1,adjusted_type_specific_negbin,0.0012240535801377,0.0002604231828641,0.00375021013525739,1.21249730072015,0.78870178835535,1.88425821404601,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,1.48355293912689,0.315632897631289,4.54525468393195,1.2844057984668,0.260653740674708,4.5916964061688,0.483552939126893,0.284405798466796,PPV23 +France.post.PCV7,9V,1212,838866,2,0,2,adjusted_type_specific_negbin,0.000542739681581876,9.77047820149844e-05,0.00199575417010017,1.21249730072015,0.78870178835535,1.88425821404601,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,0.657800494077234,0.118418195802161,2.41885405416141,2.25204995726776,0.448018408694749,8.18685213761018,0.657800494077234,0.252049957267762,PCV7 +Goroka.pre.PCV,1,2844,96207,6,1,1,adjusted_type_specific_negbin,0.000667644185795673,0.000151240877630014,0.00189718395321884,0.108412573448231,0.0462604706628933,0.249185578407515,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,1.89878006440289,0.430129055979759,5.39559116295439,0.710566494335528,0.139087209416774,2.55312751409232,0.898780064402893,0.289433505664472,PCV10 +Goroka.pre.PCV,13,2844,96207,6,45,1,adjusted_type_specific_negbin,0.0160842038541821,0.0119102787049156,0.021108132922231,0.108412573448231,0.0462604706628933,0.249185578407515,0.000646064239496631,0.000179626011284756,0.00211440991216995,3.54405372684984,2.48735345296771,5.1992340148223,45.7434757612939,33.8728326367799,60.0315300308249,0.649890367196666,0.157753010459044,2.35278580088173,0.74347576129388,0.350109632803334,No PCV +Goroka.pre.PCV,14,2844,96207,6,118,7,adjusted_type_specific_negbin,0.0413940463442447,0.0345345769673513,0.0490962052040952,0.108412573448231,0.0462604706628933,0.249185578407515,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,117.724667803032,98.216336895147,139.629607600447,10.9218753476193,4.86922357613288,25.0274199070532,0.275332196968222,3.92187534761931,PCV7 +Goroka.pre.PCV,2,2844,96207,6,2,1,adjusted_type_specific_negbin,0.00112039893805774,0.000304411067657959,0.00278040825183509,0.108412573448231,0.0462604706628933,0.249185578407515,0.0040320840401038,0.000264894385084091,0.0500576564904172,3.54405372684984,2.48735345296771,5.1992340148223,3.18641457983623,0.865745076419235,7.90748106821899,0.282378971218666,0.0162646867554981,2.68753908894054,1.18641457983623,0.717621028781334,PPV23 +Goroka.pre.PCV,20,2844,96207,6,12,0,adjusted_type_specific_negbin,0.00436204619406516,0.00239710751231218,0.00719700089392644,0.108412573448231,0.0462604706628933,0.249185578407515,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,12.4056593759213,6.81737376501585,20.4682705423268,0.208490532405131,0.0430474184941253,0.844089383773285,0.405659375921317,0.208490532405131,PPV23 +Goroka.pre.PCV,21,2844,96207,6,45,0,adjusted_type_specific_negbin,0.0159912820265628,0.011869642919183,0.0209786603945578,0.108412573448231,0.0462604706628933,0.249185578407515,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,45.4792060835446,33.7572644621565,59.6633101621225,0.198603082974445,0.0641799435505952,0.582943224697955,0.479206083544604,0.198603082974445,No PCV +Goroka.pre.PCV,29,2844,96207,6,22,0,adjusted_type_specific_negbin,0.00795093061019178,0.00514780879575334,0.0116162846142805,0.108412573448231,0.0462604706628933,0.249185578407515,6.4477890005963e-05,3.10034323663527e-06,0.000486340435351969,3.54405372684984,2.48735345296771,5.1992340148223,22.6124466553854,14.6403682151225,33.0367134430136,0.0313362443795495,0.00139411935378609,0.280924388451616,0.612446655385426,0.0313362443795495,No PCV +Goroka.pre.PCV,3,2844,96207,6,23,0,adjusted_type_specific_negbin,0.00803690152780225,0.00521460272875404,0.011696181765488,0.108412573448231,0.0462604706628933,0.249185578407515,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,22.8569479450696,14.8303301605765,33.2639409410479,1.02097630984536,0.386406484997489,2.5788016544788,0.143052054930411,1.02097630984536,PCV13 +Goroka.pre.PCV,31,2844,96207,6,14,1,adjusted_type_specific_negbin,0.0054249599824617,0.00317096622831241,0.00854196977321873,0.108412573448231,0.0462604706628933,0.249185578407515,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,15.4285861901211,9.01822795332049,24.2933620350341,0.16313203837416,0.0426599297883583,0.572880601278472,1.42858619012109,0.83686796162584,No PCV +Goroka.pre.PCV,34,2844,96207,6,44,1,adjusted_type_specific_negbin,0.0159744027225085,0.0117993126912538,0.020987405758594,0.108412573448231,0.0462604706628933,0.249185578407515,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,45.4312013428141,33.5572452939258,59.6881819774414,0.0988172033488429,0.0186830690979276,0.404202960502047,1.43120134281412,0.901182796651157,No PCV +Goroka.pre.PCV,36,2844,96207,6,1,0,adjusted_type_specific_negbin,0.000582939327434875,8.49654064477657e-05,0.00195314900624055,0.108412573448231,0.0462604706628933,0.249185578407515,2.58564926137961e-05,1.19079890067554e-06,0.00165031162715217,3.54405372684984,2.48735345296771,5.1992340148223,1.65787944722478,0.241641615937446,5.55475577374811,0.000876769195989078,1.97396118788033e-05,0.0752860468157078,0.657879447224785,0.000876769195989078,No PCV +Goroka.pre.PCV,38,2844,96207,6,21,0,adjusted_type_specific_negbin,0.00748346007878681,0.00476969313057886,0.0110822210728605,0.108412573448231,0.0462604706628933,0.249185578407515,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,21.2829604640697,13.5650072633663,31.5178367312153,0.40899813718275,0.129028159231866,1.22511647477623,0.282960464069681,0.40899813718275,No PCV +Goroka.pre.PCV,39,2844,96207,6,4,0,adjusted_type_specific_negbin,0.00159900675859733,0.000552374769907511,0.00356310473369533,0.108412573448231,0.0462604706628933,0.249185578407515,8.0894877481995e-05,1.24114385385516e-06,0.017114361194559,3.54405372684984,2.48735345296771,5.1992340148223,4.54757522145081,1.57095384561696,10.1334698626295,0.00803297609424502,9.27525400545256e-05,1.39952735714583,0.547575221450811,0.00803297609424502,No PCV +Goroka.pre.PCV,4,2844,96207,6,27,0,adjusted_type_specific_negbin,0.00942318660206005,0.00633626320864342,0.0133226535851718,0.108412573448231,0.0462604706628933,0.249185578407515,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,26.7995426962588,18.0203325653819,37.8896267962285,1.12051260502838,0.412733146220605,2.95812804379567,0.200457303741224,1.12051260502838,PCV7 +Goroka.pre.PCV,42,2844,96207,6,14,0,adjusted_type_specific_negbin,0.00514967972243209,0.00292252126603378,0.0082968762712338,0.108412573448231,0.0462604706628933,0.249185578407515,1.66572113216006e-05,1.16494987530368e-06,0.000762582274495337,3.54405372684984,2.48735345296771,5.1992340148223,14.6456891305969,8.31165048060008,23.5963161153889,0.00535125858115976,0.000276989284210426,0.260202881015975,0.645689130596857,0.00535125858115976,No PCV +Goroka.pre.PCV,43,2844,96207,6,1,0,adjusted_type_specific_negbin,0.000553533904694132,7.3848436281883e-05,0.00190530704838152,0.108412573448231,0.0462604706628933,0.249185578407515,0.000138575436726297,1.27290612976296e-06,0.0555169332326205,3.54405372684984,2.48735345296771,5.1992340148223,1.57425042495011,0.210024952785675,5.41869324559705,0.0048001340430321,2.55625809857704e-05,1.27789451761182,0.574250424950111,0.0048001340430321,No PCV +Goroka.pre.PCV,45,2844,96207,6,7,0,adjusted_type_specific_negbin,0.00268970423407476,0.00122326363153643,0.00505072427843692,0.108412573448231,0.0462604706628933,0.249185578407515,1.59311396867691e-05,1.1560837920513e-06,0.000873937490688985,3.54405372684984,2.48735345296771,5.1992340148223,7.64951884170863,3.47896176808961,14.3642598478746,0.00267726120061492,0.000134280656446322,0.1593533121153,0.649518841708629,0.00267726120061492,No PCV +Goroka.pre.PCV,46,2844,96207,6,0,3,adjusted_type_specific_negbin,0.000557268100462314,8.10358344673774e-05,0.00189584464866649,0.108412573448231,0.0462604706628933,0.249185578407515,0.0444406031297313,0.00432635280035329,0.569810674714261,3.54405372684984,2.48735345296771,5.1992340148223,1.58487047771482,0.230465913225221,5.3917821808075,1.52752415983449,0.226645724181234,7.70263903540785,1.58487047771482,1.47247584016551,No PCV +Goroka.pre.PCV,47,2844,96207,6,1,0,adjusted_type_specific_negbin,0.000552574331739199,7.33624562077079e-05,0.00190065577564436,0.108412573448231,0.0462604706628933,0.249185578407515,0.000132700228354572,1.32610965750331e-06,0.0503540995010625,3.54405372684984,2.48735345296771,5.1992340148223,1.57152139946628,0.208642825454721,5.40546502593255,0.00443792380023943,2.64272990392214e-05,1.22830838506862,0.571521399466282,0.00443792380023943,No PCV +Goroka.pre.PCV,5,2844,96207,6,5,2,adjusted_type_specific_negbin,0.00223698442566609,0.000973809705679362,0.00431902457749803,0.108412573448231,0.0462604706628933,0.249185578407515,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,6.36198370659437,2.76951480295211,12.2833058984044,1.01523390753574,0.290587757783206,3.19812270716232,1.36198370659437,0.984766092464263,PCV10 +Goroka.pre.PCV,8,2844,96207,6,9,0,adjusted_type_specific_negbin,0.0032639736057121,0.00162469215879555,0.00578457793264595,0.108412573448231,0.0462604706628933,0.249185578407515,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,9.28274093464522,4.62062449961454,16.4513396404451,0.384887431508418,0.115757403166877,1.20858896406764,0.282740934645219,0.384887431508418,PCV20 +Massachusetts.post.PCV7,1,2969,820000,3,0,1,adjusted_type_specific_negbin,0.000103758874658852,1.25098868029348e-05,0.000511345384752833,0.398519954621322,0.256257205213944,0.621964116929527,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,0.308060098862131,0.0371418539179135,1.51818444733116,1.75628046365165,0.223935798220564,8.39041890845205,0.308060098862131,0.756280463651649,PCV10 +Massachusetts.post.PCV7,10A,2969,820000,3,27,4,adjusted_type_specific_negbin,0.00904359221296226,0.00610254160789057,0.0128018308881477,0.398519954621322,0.256257205213944,0.621964116929527,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,26.850425280285,18.1184460338271,38.0086359069104,6.32826891263587,3.27643590823891,12.288283102171,0.149574719715041,2.32826891263587,PCV20 +Massachusetts.post.PCV7,11A,2969,820000,3,63,3,adjusted_type_specific_negbin,0.0218022529782061,0.0169439041539535,0.0275034528887729,0.398519954621322,0.256257205213944,0.621964116929527,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,64.730889092294,50.3064514330878,81.6577516267667,1.42912711329169,0.646751633585819,2.94198544660151,1.73088909229398,1.57087288670831,PCV20 +Massachusetts.post.PCV7,12B,2969,820000,3,0,1,adjusted_type_specific_negbin,0.000402328282450387,5.30682514871916e-05,0.00150610570106479,0.398519954621322,0.256257205213944,0.621964116929527,0.000803657589123718,7.15519052189715e-05,0.00720297300827742,3.54405372684984,2.48735345296771,5.1992340148223,1.1945126705952,0.157559638665472,4.47162782646135,0.307871540306527,0.0201681501687523,2.39339316348487,1.1945126705952,0.692128459693473,No PCV +Massachusetts.post.PCV7,13,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000463658540609599,6.59899247008538e-05,0.00159981452937192,0.398519954621322,0.256257205213944,0.621964116929527,0.000646064239496631,0.000179626011284756,0.00211440991216995,3.54405372684984,2.48735345296771,5.1992340148223,1.3766022070699,0.195924086436835,4.74984933770523,0.283870536964192,0.0321877111416932,1.45163881187383,0.376602207069898,0.283870536964192,No PCV +Massachusetts.post.PCV7,14,2969,820000,3,3,1,adjusted_type_specific_negbin,0.000844891377633319,0.000266413951308085,0.00211830347698587,0.398519954621322,0.256257205213944,0.621964116929527,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,2.50848250019333,0.790983021433705,6.28924302317105,3.48685097348521,1.07370092420412,9.50810877301768,0.491517499806675,2.48685097348521,PCV7 +Massachusetts.post.PCV7,15A,2969,820000,3,36,3,adjusted_type_specific_negbin,0.0120759289260272,0.00866155934819111,0.0162292046294352,0.398519954621322,0.256257205213944,0.621964116929527,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,35.8534329813747,25.7161697047794,48.1845085447932,4.91559409466068,2.44721886328515,9.73756454145055,0.146567018625326,1.91559409466068,No PCV +Massachusetts.post.PCV7,15B/C,2969,820000,3,74,8,adjusted_type_specific_negbin,0.0250736706472036,0.0199017362099934,0.0310679475268457,0.398519954621322,0.256257205213944,0.621964116929527,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,74.4437281515474,59.0882548074705,92.2407362072048,8.54722568573526,5.03151473831711,14.6089590935698,0.443728151547376,0.547225685735263,PCV20 +Massachusetts.post.PCV7,15F,2969,820000,3,4,0,adjusted_type_specific_negbin,0.00147951036144451,0.000510082810653523,0.00324069336236359,0.398519954621322,0.256257205213944,0.621964116929527,0.000169416469056684,1.99360904401105e-05,0.000839805104163891,3.54405372684984,2.48735345296771,5.1992340148223,4.39266626312876,1.51443586483031,9.62161859285751,0.237281634989123,0.0245632917187414,1.31798425308786,0.392666263128755,0.237281634989123,No PCV +Massachusetts.post.PCV7,16F,2969,820000,3,13,0,adjusted_type_specific_negbin,0.00422545616817258,0.00232634877039776,0.00695361274902721,0.398519954621322,0.256257205213944,0.621964116929527,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,12.5453793633044,6.90692949931096,20.6452762518618,1.6218629748228,0.661168224282593,3.76606961464275,0.454620636695612,1.6218629748228,No PCV +Massachusetts.post.PCV7,17F,2969,820000,3,8,1,adjusted_type_specific_negbin,0.0028780362968706,0.00141260380023283,0.00517578525181793,0.398519954621322,0.256257205213944,0.621964116929527,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,8.54488976540882,4.19402068289128,15.3669064126474,1.07140326434479,0.393497641500486,2.67002344404824,0.544889765408819,0.0714032643447859,PPV23 +Massachusetts.post.PCV7,18B,2969,820000,3,0,2,adjusted_type_specific_negbin,0.000568035333969649,0.000112113075916026,0.00175120618474967,0.398519954621322,0.256257205213944,0.621964116929527,0.00124537383207727,0.000230254934727611,0.00649327559125252,3.54405372684984,2.48735345296771,5.1992340148223,1.68649690655589,0.332863722394681,5.19933116252176,0.675850250662638,0.100053713943362,3.27417996785099,1.68649690655589,1.32414974933736,No PCV +Massachusetts.post.PCV7,18C,2969,820000,3,2,4,adjusted_type_specific_negbin,0.00111402902791709,0.000412531448699373,0.00250195104227685,0.398519954621322,0.256257205213944,0.621964116929527,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,3.30755218388584,1.22480587118844,7.42829264451998,2.93238440226169,1.07402154802952,7.28280747649247,1.30755218388584,1.06761559773831,PCV7 +Massachusetts.post.PCV7,18F,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000433220138222555,5.8878631613181e-05,0.00160413062126715,0.398519954621322,0.256257205213944,0.621964116929527,0.000715462278901391,6.42185069257939e-05,0.00686363084750182,3.54405372684984,2.48735345296771,5.1992340148223,1.28623059038277,0.174810657259535,4.76266381454216,0.297420474935868,0.0170512786259135,2.60208326722679,0.286230590382767,0.297420474935868,No PCV +Massachusetts.post.PCV7,19A,2969,820000,3,113,80,adjusted_type_specific_negbin,0.0386695929452055,0.032281892364026,0.0459554423464571,0.398519954621322,0.256257205213944,0.621964116929527,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,114.810021454315,95.8449384287933,136.441708326631,58.3483776838655,38.0439530424983,92.1174721740599,1.81002145431501,21.6516223161345,PCV13 +Massachusetts.post.PCV7,19F,2969,820000,3,31,2,adjusted_type_specific_negbin,0.0101454591329371,0.0070043788326225,0.0141099342288731,0.398519954621322,0.256257205213944,0.621964116929527,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,30.1218681656902,20.7960007540562,41.8923947255244,6.36842096296562,3.54064226075501,11.3987498533298,0.878131834309826,4.36842096296562,PCV7 +Massachusetts.post.PCV7,20,2969,820000,3,0,2,adjusted_type_specific_negbin,0.000655110669142996,0.000142675908941586,0.00190781123099619,0.398519954621322,0.256257205213944,0.621964116929527,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,1.94502357668556,0.423604773647569,5.66429154482767,0.484806469222144,0.0824829084934556,1.98675071168781,1.94502357668556,1.51519353077786,PPV23 +Massachusetts.post.PCV7,21,2969,820000,3,7,1,adjusted_type_specific_negbin,0.00270520457102453,0.00128124667720632,0.00496467351575904,0.398519954621322,0.256257205213944,0.621964116929527,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,8.03175237137184,3.80402138462557,14.7401156682886,0.525041445214222,0.181942155512758,1.37684392976305,1.03175237137184,0.474958554785778,No PCV +Massachusetts.post.PCV7,22F,2969,820000,3,26,14,adjusted_type_specific_negbin,0.00943144413512127,0.00654842990032537,0.0130807856611201,0.398519954621322,0.256257205213944,0.621964116929527,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,28.001957637175,19.442288374066,38.8368526278655,9.41429242190717,5.19763121445434,17.542089434905,2.00195763717504,4.58570757809283,PCV15 +Massachusetts.post.PCV7,23A,2969,820000,3,62,1,adjusted_type_specific_negbin,0.0207014511584744,0.0160079893426026,0.0262063155048468,0.398519954621322,0.256257205213944,0.621964116929527,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,61.4626084895106,47.5277203581871,77.80655073389,3.21982254635388,1.59836033974558,6.31246152863786,0.537391510489414,2.21982254635388,No PCV +Massachusetts.post.PCV7,23B,2969,820000,3,43,6,adjusted_type_specific_negbin,0.0150366581268715,0.0111650017778767,0.0197274735351839,0.398519954621322,0.256257205213944,0.621964116929527,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,44.6438379786814,33.1488902785159,58.570868925961,3.79513910016861,1.9883543307158,7.11527883805014,1.64383797868138,2.20486089983139,No PCV +Massachusetts.post.PCV7,23F,2969,820000,3,5,2,adjusted_type_specific_negbin,0.00205674703924889,0.000909612425418901,0.00391571376280103,0.398519954621322,0.256257205213944,0.621964116929527,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,6.10648195952997,2.70063929106872,11.6257541617563,1.37403543897577,0.556673697535468,3.06843275571161,1.10648195952997,0.625964561024225,PCV7 +Massachusetts.post.PCV7,25A,2969,820000,3,3,0,adjusted_type_specific_negbin,0.000896810192371978,0.000246691040567882,0.00229091442807046,0.398519954621322,0.256257205213944,0.621964116929527,0.00163929978568756,0.000579341956760081,0.00489291543751703,3.54405372684984,2.48735345296771,5.1992340148223,2.6626294611524,0.732425699446042,6.80172493694119,1.40629316157878,0.330380827575907,5.12912871396038,0.337370538847598,1.40629316157878,No PCV +Massachusetts.post.PCV7,3,2969,820000,3,11,8,adjusted_type_specific_negbin,0.0039598055113307,0.00226447761874514,0.00646131424906388,0.398519954621322,0.256257205213944,0.621964116929527,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,11.7566625631408,6.72323405005432,19.1836420054707,7.84084792812096,4.04033407325442,15.1037611569265,0.756662563140839,0.159152071879039,PCV13 +Massachusetts.post.PCV7,31,2969,820000,3,7,0,adjusted_type_specific_negbin,0.0023008955103179,0.00102315013922257,0.00436795342750622,0.398519954621322,0.256257205213944,0.621964116929527,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,6.83135877013384,3.03773276335182,12.968453726266,1.08340245134978,0.311056034316758,3.30513780615292,0.168641229866156,1.08340245134978,No PCV +Massachusetts.post.PCV7,33A,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000544103172349413,7.85711961957728e-05,0.00184714767316757,0.398519954621322,0.256257205213944,0.621964116929527,1.83415220459604e-05,1.1591301010308e-06,0.000933287511774811,3.54405372684984,2.48735345296771,5.1992340148223,1.61544231870541,0.233277881505249,5.48418144163452,0.00938250808604183,0.00030676469860575,0.519014137391477,0.615442318705407,0.00938250808604183,No PCV +Massachusetts.post.PCV7,33F,2969,820000,3,6,11,adjusted_type_specific_negbin,0.00328426039989434,0.00180395715592474,0.00552278406294465,0.398519954621322,0.256257205213944,0.621964116929527,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,9.75096912728629,5.35594879594057,16.3971458828827,4.26876769142935,2.07739226908058,8.6287155242918,3.75096912728629,6.73123230857065,PCV15 +Massachusetts.post.PCV7,34,2969,820000,3,12,0,adjusted_type_specific_negbin,0.00411990642233045,0.00224293266826705,0.00683686839392418,0.398519954621322,0.256257205213944,0.621964116929527,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,12.2320021678991,6.65926709208487,20.2986622615609,0.399840216707665,0.0810594745026379,1.41620195135518,0.232002167899111,0.399840216707665,No PCV +Massachusetts.post.PCV7,35B,2969,820000,3,65,0,adjusted_type_specific_negbin,0.0216473240733711,0.0168821464041949,0.027235310445577,0.398519954621322,0.256257205213944,0.621964116929527,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,64.2709051738388,50.1230926740546,80.8616367129181,2.75581875939396,1.17593458614772,6.18784925364562,0.729094826161202,2.75581875939396,No PCV +Massachusetts.post.PCV7,35F,2969,820000,3,26,1,adjusted_type_specific_negbin,0.00890380072248084,0.00592941352603062,0.012646983589654,0.398519954621322,0.256257205213944,0.621964116929527,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,26.4353843450456,17.6044287587849,37.5488942776827,1.30040734246767,0.531619941048306,2.95678355819042,0.435384345045616,0.300407342467671,No PCV +Massachusetts.post.PCV7,36,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000535177011265317,7.14025686964218e-05,0.00178740926099572,0.398519954621322,0.256257205213944,0.621964116929527,2.58564926137961e-05,1.19079890067554e-06,0.00165031162715217,3.54405372684984,2.48735345296771,5.1992340148223,1.58894054644672,0.211994226459676,5.30681809589629,0.0128657856680443,0.000323446878184473,0.827765200502166,0.588940546446725,0.0128657856680443,No PCV +Massachusetts.post.PCV7,37,2969,820000,3,3,0,adjusted_type_specific_negbin,0.00118891094176841,0.000352294504231419,0.00282208464937759,0.398519954621322,0.256257205213944,0.621964116929527,8.82466692072548e-05,4.22185054013693e-06,0.000564483172719643,3.54405372684984,2.48735345296771,5.1992340148223,3.52987658611042,1.04596238306308,8.37876932400207,0.0965580517934839,0.00441187790949248,0.745328063865192,0.529876586110418,0.0965580517934839,No PCV +Massachusetts.post.PCV7,38,2969,820000,3,5,2,adjusted_type_specific_negbin,0.00198413575009165,0.000836056859936241,0.00386632767656728,0.398519954621322,0.256257205213944,0.621964116929527,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,5.89089904202211,2.4822528171507,11.4791268717283,1.68273247955572,0.580612726548958,4.47281614620229,0.890899042022108,0.317267520444279,No PCV +Massachusetts.post.PCV7,4,2969,820000,3,0,3,adjusted_type_specific_negbin,0.000669495400946294,0.000187023843968224,0.00177176401070715,0.398519954621322,0.256257205213944,0.621964116929527,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,1.98773184540955,0.555273792741657,5.26036734778953,1.24304827962839,0.336141846263547,3.53844470688834,1.98773184540955,1.75695172037161,PCV7 +Massachusetts.post.PCV7,6A,2969,820000,3,27,12,adjusted_type_specific_negbin,0.0104677024160206,0.00736132141493207,0.0143960113192624,0.398519954621322,0.256257205213944,0.621964116929527,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,31.0786084731651,21.8557632809333,42.74175760689,4.43223353109624,2.60020068498823,7.58961527328156,4.07860847316515,7.56776646890376,PCV13 +Massachusetts.post.PCV7,6B,2969,820000,3,8,2,adjusted_type_specific_negbin,0.00289801369551278,0.00145161020912161,0.00513150957811407,0.398519954621322,0.256257205213944,0.621964116929527,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,8.60420266197743,4.30983071088206,15.2354519374207,2.111348531253,0.945184999888011,4.3708924895417,0.604202661977432,0.111348531253005,PCV7 +Massachusetts.post.PCV7,6C,2969,820000,3,65,1,adjusted_type_specific_negbin,0.021946099699806,0.0171207780392742,0.0276603989351788,0.398519954621322,0.256257205213944,0.621964116929527,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,65.1579700087239,50.8315899986052,82.1237244385457,1.79937416782377,0.715178913504327,4.21538666389826,0.157970008723879,0.799374167823769,No PCV +Massachusetts.post.PCV7,7C,2969,820000,3,5,1,adjusted_type_specific_negbin,0.00196048935520303,0.00081487112299474,0.00390541764178793,0.398519954621322,0.256257205213944,0.621964116929527,0.000393012283852677,0.00011306744230165,0.00121318243232636,3.54405372684984,2.48735345296771,5.1992340148223,5.82069289559781,2.41935236417138,11.5951849784684,0.739152837031971,0.181106822663132,2.59619058987612,0.820692895597809,0.260847162968029,No PCV +Massachusetts.post.PCV7,7F,2969,820000,3,21,28,adjusted_type_specific_negbin,0.00669981955917972,0.00427836638487265,0.00994503429732814,0.398519954621322,0.256257205213944,0.621964116929527,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,19.8917642712046,12.7024697966869,29.5268068287672,61.9150369083265,31.8993541458947,122.188639925723,1.10823572879541,33.9150369083265,PCV10 +Massachusetts.post.PCV7,9A,2969,820000,3,1,0,adjusted_type_specific_negbin,0.000482176394325596,6.28485729323281e-05,0.00167961970743558,0.398519954621322,0.256257205213944,0.621964116929527,0.000322376410083512,8.54282288459075e-06,0.00437510447699665,3.54405372684984,2.48735345296771,5.1992340148223,1.43158171475269,0.186597413036082,4.98679091137623,0.141562460164064,0.0032502297424815,1.82445024164727,0.431581714752695,0.141562460164064,No PCV +Massachusetts.post.PCV7,9N,2969,820000,3,4,0,adjusted_type_specific_negbin,0.00137561876208576,0.000471121098118241,0.0030664031924029,0.398519954621322,0.256257205213944,0.621964116929527,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,4.08421210463263,1.39875854031306,9.10415107824422,0.695539916413828,0.185110664414815,2.16577003882444,0.0842121046326323,0.695539916413828,PPV23 +Massachusetts.post.PCV7,9V,2969,820000,3,2,0,adjusted_type_specific_negbin,0.00060225220229374,0.000137622053239597,0.00174318812533019,0.398519954621322,0.256257205213944,0.621964116929527,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,1.78808678861011,0.408599876068363,5.17552554410534,1.20798475563448,0.266332396748719,3.85993020962464,0.211913211389886,1.20798475563448,PCV7 +Navajo.post.PCV7,1,6541,65048,6,8,22,adjusted_type_specific_negbin,0.00173193116851532,0.000987973663543418,0.00282718215505699,1,1,1,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,11.3285617732587,6.4623357332375,18.4925984762277,11.6069878423884,6.11022407283975,22.3620215138187,3.32856177325873,10.3930121576116,PCV10 +Navajo.post.PCV7,10A,6541,65048,6,85,0,adjusted_type_specific_negbin,0.0128304049671584,0.0103261620644146,0.0157019045733368,1,1,1,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,83.9236788901833,67.5434260633359,102.706157814196,3.58030642752031,1.94820064893479,6.68391055067143,1.07632110981669,3.58030642752031,PCV20 +Navajo.post.PCV7,10C,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000240084542422928,3.46125622492947e-05,0.000820062302001054,1,1,1,8.88382053940283e-05,1.2412098159882e-06,0.0208532691490767,3.54405372684984,2.48735345296771,5.1992340148223,1.57039299198837,0.226400769672637,5.36402751738889,0.00788201959852026,7.55079731409667e-05,1.40643842889668,0.570392991988371,0.00788201959852026,No PCV +Navajo.post.PCV7,10F,6541,65048,6,25,0,adjusted_type_specific_negbin,0.00390266045562828,0.00257078130960209,0.00561388065756482,1,1,1,2.03616705562456e-05,1.15719006086973e-06,0.00117849332263785,3.54405372684984,2.48735345296771,5.1992340148223,25.5273020402646,16.8154805461073,36.7203933811315,0.0308632706555505,0.00169183870244326,1.74742571522973,0.527302040264551,0.0308632706555505,No PCV +Navajo.post.PCV7,11A,6541,65048,6,92,0,adjusted_type_specific_negbin,0.0141068281713407,0.0113997194101193,0.017163897753027,1,1,1,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,92.2727630687395,74.5655646615901,112.26905520255,0.368530925178634,0.162801132644893,0.774880669023288,0.272763068739536,0.368530925178634,PCV20 +Navajo.post.PCV7,12F,6541,65048,6,25,15,adjusted_type_specific_negbin,0.00415637077938492,0.00283176459460884,0.00586405622026186,1,1,1,0.00604172772796168,0.00276457252642332,0.013992691352501,3.54405372684984,2.48735345296771,5.1992340148223,27.1868212679568,18.5225722133364,38.3567917367328,9.70203369181381,4.54145458513844,22.5086443764108,2.18682126795677,5.29796630818619,PCV20 +Navajo.post.PCV7,14,6541,65048,6,4,0,adjusted_type_specific_negbin,0.000595092990487309,0.000204379352369606,0.00134383576141403,1,1,1,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,3.89250325077749,1.33684534384959,8.79002971540918,0.981635039816421,0.314093056732475,2.49255128648852,0.107496749222513,0.981635039816421,PCV7 +Navajo.post.PCV7,15A,6541,65048,6,132,4,adjusted_type_specific_negbin,0.0203187283500325,0.0171182519488004,0.0239381062378138,1,1,1,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,132.904802137563,111.970485997103,156.57915290154,3.30675568948364,1.72020659211919,6.37932893703252,0.904802137562513,0.693244310516361,No PCV +Navajo.post.PCV7,15B/C,6541,65048,6,124,2,adjusted_type_specific_negbin,0.0189956753418653,0.0159453800749894,0.02246111899026,1,1,1,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,124.250712411141,104.298731070506,146.91817931529,2.59071039879229,1.48671685302416,4.48141486794936,0.250712411140654,0.590710398792291,PCV20 +Navajo.post.PCV7,16F,6541,65048,6,83,1,adjusted_type_specific_negbin,0.0126981305902374,0.0102000264245768,0.0155421655811254,1,1,1,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,83.0584721907426,66.7183728431569,101.661305066141,1.9624569336937,0.919252220778692,4.03337718087994,0.0584721907425774,0.962456933693697,No PCV +Navajo.post.PCV7,17F,6541,65048,6,96,1,adjusted_type_specific_negbin,0.0146537923764604,0.0119283421854085,0.017723662046256,1,1,1,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,95.8504559344273,78.0232862347568,115.93047344456,2.19341716524965,0.969678571723807,4.70606925312076,0.149544065572741,1.19341716524965,PPV23 +Navajo.post.PCV7,18C,6541,65048,6,1,0,adjusted_type_specific_negbin,0.00022228491477682,3.01514460293144e-05,0.000754652045641026,1,1,1,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,1.45396562755518,0.197220608477746,4.93617903053795,0.233618655571803,0.0301198726221801,0.921844996577833,0.453965627555181,0.233618655571803,PCV7 +Navajo.post.PCV7,19A,6541,65048,6,208,29,adjusted_type_specific_negbin,0.0321371055786364,0.0281054912313902,0.0365232567653432,1,1,1,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,210.20880758986,183.838018144524,238.89862250211,19.3742616750689,12.4796786135598,30.327389211173,2.20880758986044,9.62573832493109,PCV13 +Navajo.post.PCV7,19F,6541,65048,6,35,1,adjusted_type_specific_negbin,0.00540793363041348,0.00382491970994099,0.00735815237226085,1,1,1,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,35.3732938765346,25.018799822724,48.1296746669582,1.35300914183976,0.741638220654499,2.43896597633766,0.373293876534603,0.353009141839758,PCV7 +Navajo.post.PCV7,20,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000243732884066841,3.60439938249245e-05,0.000800098418317648,1,1,1,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,1.59425679468121,0.235763763608831,5.23344375421573,0.0707672227366225,0.0072780920718584,0.394200983489163,0.594256794681206,0.0707672227366225,PPV23 +Navajo.post.PCV7,21,6541,65048,6,88,2,adjusted_type_specific_negbin,0.0136530536331751,0.0110411384745076,0.0166585675209719,1,1,1,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,89.3046238145982,72.2200867617544,108.963690154677,1.06489890905028,0.451925417461418,2.35293734991418,1.30462381459824,0.935101090949724,No PCV +Navajo.post.PCV7,22A,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000239741027201681,3.3996901215163e-05,0.000806857613129169,1,1,1,8.5238114070162e-05,1.23227813380045e-06,0.0199848511488342,3.54405372684984,2.48735345296771,5.1992340148223,1.56814605892619,0.222373730848381,5.27765564747789,0.00765116041228371,7.29339528282689e-05,1.38806482628995,0.568146058926194,0.00765116041228371,No PCV +Navajo.post.PCV7,22F,6541,65048,6,134,4,adjusted_type_specific_negbin,0.0203945757145069,0.0171864656266386,0.0239935080614361,1,1,1,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,133.40091974859,112.416671663843,156.941536229854,8.17459080296427,4.49144516997788,15.0205772584891,0.599080251410385,4.17459080296427,PCV15 +Navajo.post.PCV7,23A,6541,65048,6,89,1,adjusted_type_specific_negbin,0.0137107547376828,0.0111172630817894,0.0167476705216218,1,1,1,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,89.6820467391833,72.7180178179847,109.546512881928,0.849512803687814,0.416340235652257,1.68270241488563,0.682046739183306,0.150487196312186,No PCV +Navajo.post.PCV7,23B,6541,65048,6,137,3,adjusted_type_specific_negbin,0.0211137842852684,0.0178621433405564,0.024723807321802,1,1,1,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,138.10526300994,116.83627959058,161.718423691907,2.13164841336804,1.12089901026401,3.94849767964891,1.10526300994047,0.868351586631959,No PCV +Navajo.post.PCV7,27,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000203047996233084,2.85421902091825e-05,0.000708693182176883,1,1,1,0.00445332639932121,0.00109948577435022,0.0190137059440571,3.54405372684984,2.48735345296771,5.1992340148223,1.3281369433606,0.186694466158263,4.63556210461899,0.347449074165937,0.0372531588497727,1.91017608661649,0.328136943360603,0.347449074165937,No PCV +Navajo.post.PCV7,3,6541,65048,6,73,10,adjusted_type_specific_negbin,0.011303588645103,0.00895530362433259,0.0140725526522989,1,1,1,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,73.9367733276185,58.5766410067594,92.0485668986872,8.96930810030515,5.23344163454829,15.5699528826496,0.936773327618482,1.03069189969485,PCV13 +Navajo.post.PCV7,31,6541,65048,6,50,1,adjusted_type_specific_negbin,0.00768369738542542,0.00578623860596551,0.0100133159709952,1,1,1,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,50.2590645980677,37.8477867216204,65.4970997662799,1.463563993682,0.500098583011013,3.88078708499509,0.259064598067702,0.463563993682001,No PCV +Navajo.post.PCV7,33A,6541,65048,6,1,0,adjusted_type_specific_negbin,0.000255484309504984,3.75499693049006e-05,0.00084395176591454,1,1,1,1.83415220459604e-05,1.1591301010308e-06,0.000933287511774811,3.54405372684984,2.48735345296771,5.1992340148223,1.6711228684721,0.245614349223355,5.52028850084701,0.00171848870276445,5.46653727721562e-05,0.107504832484451,0.6711228684721,0.00171848870276445,No PCV +Navajo.post.PCV7,33F,6541,65048,6,60,2,adjusted_type_specific_negbin,0.00909802531207034,0.00700825791212685,0.0115535212360943,1,1,1,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,59.5101835662521,45.8410150032217,75.5715824052931,4.7390060712025,2.38087235444166,9.47011822926003,0.489816433747933,2.7390060712025,PCV15 +Navajo.post.PCV7,34,6541,65048,6,89,1,adjusted_type_specific_negbin,0.0137515664774842,0.0111650222066139,0.0167334561532289,1,1,1,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,89.9489963292245,73.0304102534617,109.45353669827,0.540450061365718,0.118492630422201,1.76705208816072,0.948996329224457,0.459549938634282,No PCV +Navajo.post.PCV7,35A,6541,65048,6,55,0,adjusted_type_specific_negbin,0.00848175424194164,0.00644399453281513,0.0109229815051775,1,1,1,1.44446036923714e-05,1.13779728845997e-06,0.000584432195160938,3.54405372684984,2.48735345296771,5.1992340148223,55.4791544965402,42.1501682391437,71.4472220253659,0.0477541995739726,0.00373763880023814,1.90580340079647,0.479154496540247,0.0477541995739726,No PCV +Navajo.post.PCV7,35B,6541,65048,6,137,2,adjusted_type_specific_negbin,0.0211269605949315,0.0178153321007718,0.0247364585142031,1,1,1,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,138.191449251447,116.530087271148,161.801175141403,1.07183007444058,0.468537051842538,2.33750219830275,1.19144925144701,0.928169925559417,No PCV +Navajo.post.PCV7,35F,6541,65048,6,58,0,adjusted_type_specific_negbin,0.00888350932095121,0.0068062210098995,0.0113514109990144,1,1,1,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,58.1070344683418,44.5194916257526,74.2495793445531,0.516423503310306,0.213535136250908,1.1737038083029,0.107034468341844,0.516423503310306,No PCV +Navajo.post.PCV7,37,6541,65048,6,10,0,adjusted_type_specific_negbin,0.00162341377445157,0.000836599682238029,0.00279662998295309,1,1,1,8.82466692072548e-05,4.22185054013693e-06,0.000564483172719643,3.54405372684984,2.48735345296771,5.1992340148223,10.6187494986877,5.47219852151895,18.2927567184961,0.0545078546919741,0.00253767159948515,0.387362143325353,0.618749498687691,0.0545078546919741,No PCV +Navajo.post.PCV7,38,6541,65048,6,32,1,adjusted_type_specific_negbin,0.00491285603965254,0.00342287364273952,0.0067939630480479,1,1,1,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,32.1349913553673,22.3890164971592,44.4393122972813,1.67798187968791,0.69677283986565,3.9540322003551,0.134991355367291,0.677981879687915,No PCV +Navajo.post.PCV7,4,6541,65048,6,5,0,adjusted_type_specific_negbin,0.000788203090691565,0.00030648066365977,0.00163831855261382,1,1,1,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,5.15563641621352,2.00469002099855,10.716241652647,0.583055714785103,0.190901819544655,1.52794347923913,0.155636416213524,0.583055714785103,PCV7 +Navajo.post.PCV7,5,6541,65048,6,2,0,adjusted_type_specific_negbin,0.000300893401025981,6.60560406687214e-05,0.000877928792351374,1,1,1,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,1.96814373611094,0.432072562014107,5.74253223077034,0.857093207224103,0.169608749581025,3.12591500672165,0.0318562638890565,0.857093207224103,PCV10 +Navajo.post.PCV7,6B,6541,65048,6,4,0,adjusted_type_specific_negbin,0.000681763687877244,0.00024110310830008,0.00149622840110496,1,1,1,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,4.45941628240505,1.57705543139083,9.78682997162753,0.197795311487264,0.0631851682804194,0.50715013568628,0.459416282405055,0.197795311487264,PCV7 +Navajo.post.PCV7,7C,6541,65048,6,60,1,adjusted_type_specific_negbin,0.00922447148272639,0.00707465857013102,0.0117461372171856,1,1,1,0.000393012283852677,0.00011306744230165,0.00121318243232636,3.54405372684984,2.48735345296771,5.1992340148223,60.3372679685133,46.275341707227,76.8314835376107,1.41324574529531,0.400222437444057,4.39809159844131,0.337267968513338,0.413245745295308,No PCV +Navajo.post.PCV7,7F,6541,65048,6,13,24,adjusted_type_specific_negbin,0.00267941946683502,0.00168626850836093,0.00400558938173882,1,1,1,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,17.5260827325679,11.0298823131888,26.2005601459536,9.89430142995327,5.51876517873501,17.9555322396768,4.52608273256786,14.1056985700467,PCV10 +Navajo.post.PCV7,8,6541,65048,6,11,1,adjusted_type_specific_negbin,0.00174595026203292,0.000949859838195416,0.00290837975109752,1,1,1,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,11.4202606639573,6.21303320163622,19.0237119519289,1.2926480234613,0.517287409513413,3.12626153543071,0.420260663957329,0.292648023461296,PCV20 +Navajo.post.PCV7,9N,6541,65048,6,9,0,adjusted_type_specific_negbin,0.00143121813228834,0.000706345854659752,0.00254485875013325,1,1,1,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,9.36159780329805,4.62020823532944,16.6459210846216,0.288753267035269,0.0980158136679594,0.808402260788565,0.36159780329805,0.288753267035269,PPV23 +Navajo.post.PCV7,9V,6541,65048,6,7,0,adjusted_type_specific_negbin,0.00106127178216199,0.000481403439093832,0.00200420810556797,1,1,1,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,6.94177872712157,3.14885989511275,13.1095252185201,0.846220636046899,0.318034967188256,2.04711475317276,0.0582212728784324,0.846220636046899,PCV7 +Netherlands.post.PCV10,1,659,222671,4,3,3,adjusted_type_specific_negbin,0.00334709423797445,0.00105172601955574,0.00869768762710844,0.168552603989142,0.0982487193306246,0.289513041381206,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,2.20573510282516,0.69308744688723,5.73177614626446,8.53853028205202,2.6945137635005,25.6163652572476,0.794264897174839,5.53853028205202,PCV10 +Netherlands.post.PCV10,10A,659,222671,4,13,4,adjusted_type_specific_negbin,0.0221288466297476,0.0132599170462704,0.0346276894254066,0.168552603989142,0.0982487193306246,0.289513041381206,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,14.5829099290037,8.73828533349219,22.8196473313429,2.37603963636376,1.11549698007137,4.95303559551749,1.58290992900367,1.62396036363624,PCV20 +Netherlands.post.PCV10,10B,659,222671,4,2,1,adjusted_type_specific_negbin,0.00481076759815348,0.00138522685320297,0.0118384139525048,0.168552603989142,0.0982487193306246,0.289513041381206,0.000502204985915827,8.47222594103277e-05,0.00253825696624574,3.54405372684984,2.48735345296771,5.1992340148223,3.17029584718315,0.912864496260756,7.80151479470069,0.35601842616481,0.0460104049657685,1.87487565717126,1.17029584718315,0.64398157383519,No PCV +Netherlands.post.PCV10,11A,659,222671,4,31,0,adjusted_type_specific_negbin,0.0472920715307722,0.0327702271584294,0.0655481326910225,0.168552603989142,0.0982487193306246,0.289513041381206,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,31.1654751387789,21.595579697405,43.1962194433838,0.474131219560965,0.192798042810351,1.08798625555033,0.165475138778863,0.474131219560965,PCV20 +Netherlands.post.PCV10,14,659,222671,4,0,1,adjusted_type_specific_negbin,0.00129817276583633,0.000176865553710212,0.00482157139306011,0.168552603989142,0.0982487193306246,0.289513041381206,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,0.85549585268614,0.11655439989503,3.17741554802661,0.8185126966047,0.110994647575763,3.18008572155442,0.85549585268614,0.1814873033953,PCV7 +Netherlands.post.PCV10,15A,659,222671,4,8,0,adjusted_type_specific_negbin,0.0121624677298849,0.00578983744007041,0.0222700919473881,0.168552603989142,0.0982487193306246,0.289513041381206,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,8.01506623399415,3.8155028730064,14.6759905933288,0.754555782163836,0.282265675769856,1.87957765427698,0.0150662339941512,0.754555782163836,No PCV +Netherlands.post.PCV10,15B/C,659,222671,4,28,2,adjusted_type_specific_negbin,0.0431562701959987,0.0299185075919808,0.0597541260146367,0.168552603989142,0.0982487193306246,0.289513041381206,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,28.4399820591631,19.7162965031154,39.3779690436456,2.25412075053159,1.14986933879161,4.34875349703888,0.439982059163142,0.254120750531591,PCV20 +Netherlands.post.PCV10,15F,659,222671,4,1,0,adjusted_type_specific_negbin,0.00243180154641324,0.000342662949632523,0.0080301907666806,0.168552603989142,0.0982487193306246,0.289513041381206,0.000169416469056684,1.99360904401105e-05,0.000839805104163891,3.54405372684984,2.48735345296771,5.1992340148223,1.60255721908633,0.225814883807833,5.29189571524251,0.0571887914353698,0.00371703267679531,0.464176110334573,0.602557219086326,0.0571887914353698,No PCV +Netherlands.post.PCV10,16F,659,222671,4,10,1,adjusted_type_specific_negbin,0.016204897081135,0.00850298728134976,0.0271933733500192,0.168552603989142,0.0982487193306246,0.289513041381206,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,10.679027176468,5.60346861840949,17.9204330376626,0.95477182336276,0.368642757186671,2.31350726846632,0.679027176467972,0.0452281766372395,No PCV +Netherlands.post.PCV10,17F,659,222671,4,6,1,adjusted_type_specific_negbin,0.0105690950908784,0.00476523652936338,0.0199126332510246,0.168552603989142,0.0982487193306246,0.289513041381206,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,6.96503366488885,3.14029087285047,13.1224253124252,0.602310713930931,0.199869787369489,1.61510473231687,0.96503366488885,0.397689286069069,PPV23 +Netherlands.post.PCV10,18C,659,222671,4,0,1,adjusted_type_specific_negbin,0.00152761804282387,0.000216703657742484,0.00547757355192281,0.168552603989142,0.0982487193306246,0.289513041381206,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,1.00670029022093,0.142807710452297,3.60972097071713,0.621361070502592,0.0881741651795881,2.36194833966564,1.00670029022093,0.378638929497408,PCV7 +Netherlands.post.PCV10,19A,659,222671,4,41,5,adjusted_type_specific_negbin,0.0606210172657425,0.0443863169835941,0.0803587976425647,0.168552603989142,0.0982487193306246,0.289513041381206,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,39.9492503781243,29.2505828921885,52.9564476464501,13.9959556313898,7.81237094856054,25.3321339936143,1.0507496218757,8.99595563138979,PCV13 +Netherlands.post.PCV10,19F,659,222671,4,5,1,adjusted_type_specific_negbin,0.00877613902227825,0.00365898214466615,0.0173722285219005,0.168552603989142,0.0982487193306246,0.289513041381206,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,5.78347561568136,2.41126923333499,11.4482985959324,0.836041770602893,0.306414226567088,2.01403240508543,0.783475615681364,0.163958229397107,PCV7 +Netherlands.post.PCV10,21,659,222671,4,14,0,adjusted_type_specific_negbin,0.0213784156082447,0.0122177255853554,0.0340713173313209,0.168552603989142,0.0982487193306246,0.289513041381206,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,14.0883758858333,8.05148116074923,22.4529981213405,0.638977807815577,0.232298617519862,1.62729646030891,0.0883758858332655,0.638977807815577,No PCV +Netherlands.post.PCV10,22F,659,222671,4,5,2,adjusted_type_specific_negbin,0.00920389236386948,0.00407188599726071,0.017599563642523,0.168552603989142,0.0982487193306246,0.289513041381206,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,6.06536506778999,2.68337287219481,11.5981124404226,1.40339566652907,0.537220383322424,3.33893852759151,1.06536506778999,0.596604333470929,PCV15 +Netherlands.post.PCV10,23A,659,222671,4,18,1,adjusted_type_specific_negbin,0.0286005185114241,0.017710136547712,0.0429453752484197,0.168552603989142,0.0982487193306246,0.289513041381206,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,18.8477416990285,11.6709799849422,28.3010022887086,0.678615063975348,0.285593422620141,1.52904515209339,0.847741699028493,0.321384936024652,No PCV +Netherlands.post.PCV10,23B,659,222671,4,45,3,adjusted_type_specific_negbin,0.0694852282957978,0.0518253003670051,0.0906007201066869,0.168552603989142,0.0982487193306246,0.289513041381206,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,45.7907654469307,34.1528729418564,59.7058745503067,2.6932285105067,1.30455504626998,5.37498538871743,0.790765446930749,0.3067714894933,No PCV +Netherlands.post.PCV10,23F,659,222671,4,0,1,adjusted_type_specific_negbin,0.00212528075405125,0.000302682034483281,0.00715229817948685,0.168552603989142,0.0982487193306246,0.289513041381206,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,1.40056001691977,0.199467460724482,4.71336450028184,0.217826543808701,0.0298159718577694,0.82066481894466,1.40056001691977,0.782173456191299,PCV7 +Netherlands.post.PCV10,24F,659,222671,4,5,2,adjusted_type_specific_negbin,0.00810816923712476,0.00344147407228268,0.0160888700775661,0.168552603989142,0.0982487193306246,0.289513041381206,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,5.34328352726522,2.26793141363429,10.6025653811161,2.6456311625618,0.945543044390559,6.91659579124394,0.343283527265219,0.645631162561805,No PCV +Netherlands.post.PCV10,27,659,222671,4,0,2,adjusted_type_specific_negbin,0.00184849983371817,0.00033615209051884,0.00628086491554817,0.168552603989142,0.0982487193306246,0.289513041381206,0.00445332639932121,0.00109948577435022,0.0190137059440571,3.54405372684984,2.48735345296771,5.1992340148223,1.21816139042028,0.221524227651915,4.13908997934624,1.21545915899039,0.218461530867007,5.07807574580146,1.21816139042028,0.784540841009614,No PCV +Netherlands.post.PCV10,3,659,222671,4,2,5,adjusted_type_specific_negbin,0.00685569033829459,0.00283315230829374,0.0138924528216575,0.168552603989142,0.0982487193306246,0.289513041381206,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,4.51789993293613,1.86704737116557,9.15512640947231,2.07782115955727,0.820630756291974,4.7269774528882,2.51789993293613,2.92217884044273,PCV13 +Netherlands.post.PCV10,31,659,222671,4,2,0,adjusted_type_specific_negbin,0.00366221772540152,0.000817726992918025,0.00985175038929554,0.168552603989142,0.0982487193306246,0.289513041381206,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,2.4134014810396,0.538882088332978,6.49230350654576,0.261313651259367,0.0454305468154856,1.02564604566062,0.413401481039604,0.261313651259367,No PCV +Netherlands.post.PCV10,33A,659,222671,4,1,0,adjusted_type_specific_negbin,0.00249511254747953,0.000356355125835669,0.00829839367594407,0.168552603989142,0.0982487193306246,0.289513041381206,1.83415220459604e-05,1.1591301010308e-06,0.000933287511774811,3.54405372684984,2.48735345296771,5.1992340148223,1.64427916878901,0.234838027925706,5.46864143244714,0.00665633781196699,0.000204177646132347,0.379228281606487,0.644279168789013,0.00665633781196699,No PCV +Netherlands.post.PCV10,33F,659,222671,4,7,2,adjusted_type_specific_negbin,0.011379868232895,0.00539098716226737,0.02084849076893,0.168552603989142,0.0982487193306246,0.289513041381206,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,7.4993331654778,3.5526605399342,13.7391554167249,2.25808372646572,0.88548958717092,5.39615909180089,0.4993331654778,0.258083726465718,PCV15 +Netherlands.post.PCV10,34,659,222671,4,0,1,adjusted_type_specific_negbin,0.00244906271819827,0.000360631696814431,0.0080737640398975,0.168552603989142,0.0982487193306246,0.289513041381206,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,1.61393233129266,0.23765628820071,5.32061050229245,0.0347999112159721,0.00335879389731454,0.207007718218662,1.61393233129266,0.965200088784028,No PCV +Netherlands.post.PCV10,35B,659,222671,4,12,0,adjusted_type_specific_negbin,0.0186614474561115,0.0102968730756046,0.0306362801356678,0.168552603989142,0.0982487193306246,0.289513041381206,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,12.2978938735775,6.78563935682343,20.1893086094051,0.362080578224284,0.128105099056518,0.962371433298662,0.297893873577459,0.362080578224284,No PCV +Netherlands.post.PCV10,35F,659,222671,4,12,0,adjusted_type_specific_negbin,0.018600812594556,0.010210836622062,0.0306180712045281,0.168552603989142,0.0982487193306246,0.289513041381206,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,12.2579354998124,6.72894133393887,20.177308923784,0.414570618153619,0.143394472856336,1.0788823837897,0.257935499812419,0.414570618153619,No PCV +Netherlands.post.PCV10,37,659,222671,4,1,0,adjusted_type_specific_negbin,0.00246373149341908,0.000345602037231832,0.00829734742038211,0.168552603989142,0.0982487193306246,0.289513041381206,8.82466692072548e-05,4.22185054013693e-06,0.000564483172719643,3.54405372684984,2.48735345296771,5.1992340148223,1.62359905416317,0.227751742535777,5.46795195003181,0.0292784272564899,0.00102266425684219,0.302092994625421,0.623599054163175,0.0292784272564899,No PCV +Netherlands.post.PCV10,38,659,222671,4,4,0,adjusted_type_specific_negbin,0.00606701911214293,0.00206985675967442,0.0137329308276139,0.168552603989142,0.0982487193306246,0.289513041381206,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,3.99816559490219,1.36403560462544,9.05000141539758,0.789011903563942,0.215222966767508,2.4479453774396,0.00183440509781008,0.789011903563942,No PCV +Netherlands.post.PCV10,4,659,222671,4,0,1,adjusted_type_specific_negbin,0.00170315415694297,0.000232082160280249,0.00606994496346705,0.168552603989142,0.0982487193306246,0.289513041381206,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,1.12237858942542,0.152942143624684,4.00009373092479,0.485666683923227,0.0647564041439566,1.92299797310829,1.12237858942542,0.514333316076773,PCV7 +Netherlands.post.PCV10,6A,659,222671,4,2,0,adjusted_type_specific_negbin,0.00374913553491679,0.000848255811508079,0.0100280990404985,0.168552603989142,0.0982487193306246,0.289513041381206,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,2.47068031751017,0.559000579783824,6.60851726768854,0.240311308025368,0.0508622035607868,0.742807459727451,0.470680317510167,0.240311308025368,PCV13 +Netherlands.post.PCV10,6C,659,222671,4,44,2,adjusted_type_specific_negbin,0.0689040332417223,0.0513172091826282,0.0896472454051814,0.168552603989142,0.0982487193306246,0.289513041381206,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,45.407757906295,33.818040851352,59.0775347220146,0.862280213426137,0.329593807840549,2.09833584882112,1.40775790629496,1.13771978657386,No PCV +Netherlands.post.PCV10,7F,659,222671,4,3,2,adjusted_type_specific_negbin,0.00375880199301377,0.00119920259971958,0.00934702474900028,0.168552603989142,0.0982487193306246,0.289513041381206,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,2.47705051339608,0.790274513215205,6.15968930959119,5.29328469296269,1.66858839249852,15.2079267648802,0.522949486603923,3.29328469296269,PCV10 +Netherlands.post.PCV10,8,659,222671,4,0,2,adjusted_type_specific_negbin,0.00261250199140928,0.000576297751379475,0.00752523753901967,0.168552603989142,0.0982487193306246,0.289513041381206,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,1.72163881233872,0.379780218159074,4.95913153821397,0.743540283865628,0.152783870137273,2.4955439695354,1.72163881233872,1.25645971613437,PCV20 +Netherlands.post.PCV10,9N,659,222671,4,3,0,adjusted_type_specific_negbin,0.00502358380656163,0.00150121683072386,0.0120297157958595,0.168552603989142,0.0982487193306246,0.289513041381206,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,3.31054172852411,0.989301891447021,7.92758270947138,0.389130503444205,0.0923315130155858,1.31410793101868,0.310541728524115,0.389130503444205,PPV23 +Netherlands.post.PCV10,9V,659,222671,4,0,1,adjusted_type_specific_negbin,0.00169122468845503,0.000242610422705875,0.00579989119001152,0.168552603989142,0.0982487193306246,0.289513041381206,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,1.11451706969186,0.159880268563171,3.82212829421759,0.518455105239157,0.0710983059050768,1.98533959466124,1.11451706969186,0.481544894760843,PCV7 +Netherlands.post.PCV7,1,660,232251,4,2,9,adjusted_type_specific_negbin,0.00408459335796662,0.0015446435529896,0.0094092733987899,0.147807643076475,0.0906259657836259,0.244533879779519,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,2.69583161625797,1.01946474497313,6.21012044320133,9.57532739122608,3.76430885525213,24.044918544294,0.695831616257971,0.575327391226082,PCV10 +Netherlands.post.PCV7,10A,660,232251,4,20,8,adjusted_type_specific_negbin,0.0346838409271145,0.023115998533161,0.0499442740999402,0.147807643076475,0.0906259657836259,0.244533879779519,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,22.8913350118956,15.2565590318863,32.9632209059605,3.41312139917039,1.75866535443823,6.57691874560857,2.89133501189559,4.58687860082961,PCV20 +Netherlands.post.PCV7,11A,660,232251,4,36,0,adjusted_type_specific_negbin,0.054840622459357,0.0391516723617438,0.0737519989514496,0.147807643076475,0.0906259657836259,0.244533879779519,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,36.1948108231756,25.8401037587509,48.6763193079567,0.502969583043721,0.212386854658423,1.10878135553738,0.194810823175615,0.502969583043721,PCV20 +Netherlands.post.PCV7,12F,660,232251,4,1,0,adjusted_type_specific_negbin,0.0013352222371773,0.000181917842397086,0.00506184609859473,0.147807643076475,0.0906259657836259,0.244533879779519,0.00604172772796168,0.00276457252642332,0.013992691352501,3.54405372684984,2.48735345296771,5.1992340148223,0.881246676537016,0.120065775982077,3.34081842507252,1.10071322346253,0.147426564648796,4.76930263893395,0.118753323462984,1.10071322346253,PCV20 +Netherlands.post.PCV7,14,660,232251,4,2,0,adjusted_type_specific_negbin,0.00254915430137449,0.000549768570844287,0.00758849478169104,0.147807643076475,0.0906259657836259,0.244533879779519,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,1.68244183890717,0.362847256757229,5.00840655591609,1.47502346238166,0.307141181353453,4.68136388184698,0.317558161092833,1.47502346238166,PCV7 +Netherlands.post.PCV7,15A,660,232251,4,2,2,adjusted_type_specific_negbin,0.00627218970362468,0.00214571077331772,0.0139469637033659,0.147807643076475,0.0906259657836259,0.244533879779519,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,4.13964520439229,1.41616911038969,9.20499604422147,0.355048597731783,0.104197146855927,0.992760968586414,2.13964520439229,1.64495140226822,No PCV +Netherlands.post.PCV7,15B/C,660,232251,4,29,2,adjusted_type_specific_negbin,0.0447247260285199,0.0308321896316145,0.0620842596181676,0.147807643076475,0.0906259657836259,0.244533879779519,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,29.5183191788231,20.3492451568656,40.9756113479906,2.13794807458009,1.12214314353515,4.06558173983838,0.51831917882312,0.137948074580095,PCV20 +Netherlands.post.PCV7,16F,660,232251,4,12,3,adjusted_type_specific_negbin,0.0211828740731373,0.0122792897143391,0.033555169454829,0.147807643076475,0.0906259657836259,0.244533879779519,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,13.9806968882706,8.10433121146381,22.1464118401872,1.14622761904219,0.473958940457506,2.58071732608516,1.98069688827063,1.85377238095781,No PCV +Netherlands.post.PCV7,17F,660,232251,4,9,2,adjusted_type_specific_negbin,0.0159334062666563,0.00845265193258813,0.0271681630402762,0.147807643076475,0.0906259657836259,0.244533879779519,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,10.5160481359931,5.57875027550817,17.9309876065823,0.832973730389598,0.313618953363749,2.06846193433901,1.51604813599315,1.1670262696104,PPV23 +Netherlands.post.PCV7,18C,660,232251,4,2,2,adjusted_type_specific_negbin,0.00443816768679153,0.00146416254837994,0.0105176545480509,0.147807643076475,0.0906259657836259,0.244533879779519,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,2.92919067328241,0.966347281930758,6.94165200171363,1.64242858438421,0.5078767303754,4.48094832666152,0.929190673282412,0.357571415615792,PCV7 +Netherlands.post.PCV7,19A,660,232251,4,68,10,adjusted_type_specific_negbin,0.101712359386436,0.080839775553608,0.125433757867132,0.147807643076475,0.0906259657836259,0.244533879779519,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,67.1301571950475,53.3542518653813,82.7862801923072,21.5181592277922,12.7512061344016,36.905500838758,0.869842804952526,11.5181592277922,PCV13 +Netherlands.post.PCV7,19F,660,232251,4,8,1,adjusted_type_specific_negbin,0.0129807587980271,0.00634451688228366,0.0230873864043004,0.147807643076475,0.0906259657836259,0.244533879779519,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,8.56730080669788,4.18738114230722,15.2376750268383,1.13933647659165,0.483874176498836,2.45428406527435,0.567300806697883,0.139336476591645,PCV7 +Netherlands.post.PCV7,21,660,232251,4,16,0,adjusted_type_specific_negbin,0.0243544625339016,0.0145328343142258,0.0378100443809162,0.147807643076475,0.0906259657836259,0.244533879779519,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,16.0739452723751,9.591670647389,24.9546292914047,0.66693293795106,0.246376873012661,1.66131305901213,0.0739452723750809,0.66693293795106,No PCV +Netherlands.post.PCV7,22F,660,232251,4,7,4,adjusted_type_specific_negbin,0.0136148593478724,0.00710453303924627,0.02352985805067,0.147807643076475,0.0906259657836259,0.244533879779519,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,8.98580716959577,4.68899180590254,15.5297063134422,1.90896464348454,0.846344394838808,4.11503456633816,1.98580716959577,2.09103535651546,PCV15 +Netherlands.post.PCV7,23A,660,232251,4,11,0,adjusted_type_specific_negbin,0.0171346281394986,0.00913361801824897,0.0287483056589666,0.147807643076475,0.0906259657836259,0.244533879779519,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,11.3088545720691,6.02818789204432,18.973881734918,0.372331693350109,0.148240168546,0.867948624140754,0.30885457206907,0.372331693350109,No PCV +Netherlands.post.PCV7,23B,660,232251,4,24,1,adjusted_type_specific_negbin,0.036972022053464,0.024622085007249,0.0528618136810603,0.147807643076475,0.0906259657836259,0.244533879779519,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,24.4015345552863,16.2505761047843,34.8887970294998,1.31147033334744,0.617372546041216,2.69722021001512,0.401534555286268,0.311470333347441,No PCV +Netherlands.post.PCV7,23F,660,232251,4,2,0,adjusted_type_specific_negbin,0.00357640456954133,0.000822420034799486,0.00978381243455839,0.147807643076475,0.0906259657836259,0.244533879779519,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,2.36042701589728,0.542797222967661,6.45731620680854,0.336083676944843,0.0725895751246246,1.04130173457981,0.360427015897279,0.336083676944843,PCV7 +Netherlands.post.PCV7,24B,660,232251,4,0,1,adjusted_type_specific_negbin,0.00133594851863238,0.000130282297018142,0.0056407990194178,0.147807643076475,0.0906259657836259,0.244533879779519,0.00349173287124971,0.000414261332271996,0.0415103510785451,3.54405372684984,2.48735345296771,5.1992340148223,0.881726022297368,0.0859863160319736,3.72292735281575,0.63478835237234,0.055653606291965,4.10469884819466,0.881726022297368,0.36521164762766,No PCV +Netherlands.post.PCV7,24F,660,232251,4,3,1,adjusted_type_specific_negbin,0.00501055056682931,0.00167276104305658,0.0117038204041347,0.147807643076475,0.0906259657836259,0.244533879779519,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,3.30696337410734,1.10402228841734,7.72452146672891,1.50495428392476,0.439222417325741,4.38838463279836,0.306963374107342,0.504954283924759,No PCV +Netherlands.post.PCV7,27,660,232251,4,0,3,adjusted_type_specific_negbin,0.00254435009223101,0.000573231759871012,0.00739846210176657,0.147807643076475,0.0906259657836259,0.244533879779519,0.00445332639932121,0.00109948577435022,0.0190137059440571,3.54405372684984,2.48735345296771,5.1992340148223,1.67927106087247,0.378332961514868,4.88298498716594,1.51378334394452,0.345685620953391,5.63738220626109,1.67927106087247,1.48621665605548,No PCV +Netherlands.post.PCV7,3,660,232251,4,8,3,adjusted_type_specific_negbin,0.0127582806877738,0.00649850144354939,0.0225476082312177,0.147807643076475,0.0906259657836259,0.244533879779519,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,8.42046525393069,4.28901095274259,14.8814214326037,3.53711832262316,1.61412296898298,7.62276124993262,0.420465253930693,0.53711832262316,PCV13 +Netherlands.post.PCV7,31,660,232251,4,1,0,adjusted_type_specific_negbin,0.00228503059876121,0.000328488562523307,0.00769719271582356,0.147807643076475,0.0906259657836259,0.244533879779519,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,1.5081201951824,0.216802451265383,5.08014719244355,0.148746128862353,0.0173195328775889,0.716895534828488,0.508120195182399,0.148746128862353,No PCV +Netherlands.post.PCV7,33A,660,232251,4,2,0,adjusted_type_specific_negbin,0.00395850401075801,0.000912334867623562,0.0106994431280756,0.147807643076475,0.0906259657836259,0.244533879779519,1.83415220459604e-05,1.1591301010308e-06,0.000933287511774811,3.54405372684984,2.48735345296771,5.1992340148223,2.61261264710029,0.602141012631551,7.06163246452993,0.00964947661194738,0.00037136543401759,0.519486270787292,0.612612647100286,0.00964947661194738,No PCV +Netherlands.post.PCV7,33F,660,232251,4,7,1,adjusted_type_specific_negbin,0.0107030432034294,0.00480623739567312,0.0199693530172908,0.147807643076475,0.0906259657836259,0.244533879779519,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,7.06400851426339,3.17211668114426,13.1797729914119,1.94792787624907,0.740993740885564,4.7349303695031,0.0640085142633922,0.947927876249071,PCV15 +Netherlands.post.PCV7,35B,660,232251,4,9,0,adjusted_type_specific_negbin,0.0142801487563497,0.00710812951164101,0.0251851265475174,0.147807643076475,0.0906259657836259,0.244533879779519,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,9.42489817919083,4.69136547768307,16.6221835213615,0.253150567626894,0.0850084107755799,0.680250720218691,0.424898179190826,0.253150567626894,No PCV +Netherlands.post.PCV7,35F,660,232251,4,17,2,adjusted_type_specific_negbin,0.0284011722974949,0.0175786888859026,0.0428413140301789,0.147807643076475,0.0906259657836259,0.244533879779519,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,18.7447737163466,11.6019346646957,28.2752672599181,0.580484299224153,0.226909210560112,1.39019376712941,1.74477371634665,1.41951570077585,No PCV +Netherlands.post.PCV7,36,660,232251,4,1,0,adjusted_type_specific_negbin,0.00246735101827675,0.000349361948876539,0.00824842608395856,0.147807643076475,0.0906259657836259,0.244533879779519,2.58564926137961e-05,1.19079890067554e-06,0.00165031162715217,3.54405372684984,2.48735345296771,5.1992340148223,1.62845167206266,0.230578886258516,5.44396121541265,0.00819428652406802,0.000203441996559819,0.572357674070939,0.628451672062655,0.00819428652406802,No PCV +Netherlands.post.PCV7,38,660,232251,4,3,0,adjusted_type_specific_negbin,0.00476316123454966,0.00138136459560821,0.011695723811724,0.147807643076475,0.0906259657836259,0.244533879779519,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,3.14368641480278,0.911700633101418,7.71917771573784,0.569377182813413,0.135960100250128,1.84549023508584,0.143686414802778,0.569377182813413,No PCV +Netherlands.post.PCV7,4,660,232251,4,1,0,adjusted_type_specific_negbin,0.00187618524414856,0.000273940480696604,0.00645673362173946,0.147807643076475,0.0906259657836259,0.244533879779519,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,1.23828226113805,0.180800717259758,4.26144419034804,0.49191284573733,0.0674842923271871,1.89942856661776,0.238282261138047,0.49191284573733,PCV7 +Netherlands.post.PCV7,42,660,232251,4,1,0,adjusted_type_specific_negbin,0.0025046576958902,0.000354882903874393,0.00825145773757724,0.147807643076475,0.0906259657836259,0.244533879779519,1.66572113216006e-05,1.16494987530368e-06,0.000762582274495337,3.54405372684984,2.48735345296771,5.1992340148223,1.65307407928753,0.234222716557099,5.44596210680098,0.00547844370887947,0.000181670178023987,0.288626305670157,0.653074079287534,0.00547844370887947,No PCV +Netherlands.post.PCV7,6A,660,232251,4,25,0,adjusted_type_specific_negbin,0.0367586626651053,0.0245342598781156,0.0525534375504177,0.147807643076475,0.0906259657836259,0.244533879779519,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,24.2607173589695,16.1926115195563,34.6852687832757,2.18369499172388,1.14019022670275,4.17781809068294,0.739282641030524,2.18369499172388,PCV13 +Netherlands.post.PCV7,6B,660,232251,4,9,0,adjusted_type_specific_negbin,0.0131303487293773,0.00655166939832462,0.023323497052418,0.147807643076475,0.0906259657836259,0.244533879779519,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,8.66603016138899,4.32410180289425,15.3935080545959,1.3401221155542,0.57101822766205,2.93828441383618,0.333969838611011,1.3401221155542,PCV7 +Netherlands.post.PCV7,6C,660,232251,4,14,0,adjusted_type_specific_negbin,0.0217804437608647,0.0125446389392188,0.0348412555855656,0.147807643076475,0.0906259657836259,0.244533879779519,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,14.3750928821707,8.27946169988442,22.9952286864733,0.248028423817747,0.0853968902195191,0.6715861349147,0.375092882170676,0.248028423817747,No PCV +Netherlands.post.PCV7,7F,660,232251,4,4,13,adjusted_type_specific_negbin,0.00822051670640794,0.00385485996679026,0.0155417301039764,0.147807643076475,0.0906259657836259,0.244533879779519,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,5.42554102622924,2.54420757808157,10.2575418686244,10.6149941827402,4.97030071109626,22.7585650557042,1.42554102622924,2.3850058172598,PCV10 +Netherlands.post.PCV7,8,660,232251,4,5,4,adjusted_type_specific_negbin,0.00984433105587758,0.00458288165966759,0.0184594568021934,0.147807643076475,0.0906259657836259,0.244533879779519,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,6.4972584968792,3.02470189538061,12.1832414894477,2.56423625564963,1.00425486833145,6.25770906019277,1.4972584968792,1.43576374435037,PCV20 +Netherlands.post.PCV7,9N,660,232251,4,2,0,adjusted_type_specific_negbin,0.00362497784307491,0.000845312256545945,0.00982616275033174,0.147807643076475,0.0906259657836259,0.244533879779519,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,2.39248537642944,0.557906089320324,6.48526741521895,0.257061122724286,0.0503339921597164,0.943555081347287,0.392485376429441,0.257061122724286,PPV23 +Netherlands.post.PCV7,9V,660,232251,4,1,1,adjusted_type_specific_negbin,0.00278893695583665,0.000623378400828722,0.00792798083295088,0.147807643076475,0.0906259657836259,0.244533879779519,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,1.84069839085219,0.411429744546957,5.23246734974758,0.781510954602105,0.164586494228354,2.56760646725752,0.840698390852188,0.218489045397895,PCV7 +Netherlands.pre.PCV,1,321,250924,2,1,4,adjusted_type_specific_negbin,0.00313383469292839,0.000831631350844037,0.00987604152027021,0.244496875493983,0.148468880710923,0.406072957492,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,1.00596093643001,0.266953663620936,3.17020932800674,6.56772625895248,1.87852867149095,20.9063965555021,0.00596093643001216,2.56772625895248,PCV10 +Netherlands.pre.PCV,10A,321,250924,2,1,1,adjusted_type_specific_negbin,0.00637870441528213,0.00143440952500282,0.0175071316464978,0.244496875493983,0.148468880710923,0.406072957492,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,2.04756411730556,0.460445457525907,5.61978925852578,0.556827163732147,0.114550376384304,1.73203601875122,1.04756411730556,0.443172836267853,PCV20 +Netherlands.pre.PCV,11A,321,250924,2,10,0,adjusted_type_specific_negbin,0.0323055961084689,0.0168444494684319,0.0550263812264811,0.244496875493983,0.148468880710923,0.406072957492,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,10.3700963508185,5.40706827936663,17.6634683737004,0.263824716196395,0.0969253794889812,0.650116591578409,0.370096350818528,0.263824716196395,PCV20 +Netherlands.pre.PCV,14,321,250924,2,8,28,adjusted_type_specific_negbin,0.0331473212985446,0.0190404170222548,0.0536609419010401,0.244496875493983,0.148468880710923,0.406072957492,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,10.6402901368328,6.11197386414378,17.2251623502339,17.0825090550566,9.24946240183832,31.4220420428966,2.64029013683282,10.9174909449434,PCV7 +Netherlands.pre.PCV,15A,321,250924,2,2,0,adjusted_type_specific_negbin,0.00724024821258492,0.00166310268473911,0.0197701990823736,0.244496875493983,0.148468880710923,0.406072957492,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,2.32411967623976,0.533855961801254,6.34623390544192,0.365466155085818,0.0753759455065692,1.22029036567632,0.324119676239759,0.365466155085818,No PCV +Netherlands.pre.PCV,15B/C,321,250924,2,10,2,adjusted_type_specific_negbin,0.0342880409468368,0.0188116969698974,0.0567133552662573,0.244496875493983,0.148468880710923,0.406072957492,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,11.0064611439346,6.03855472733706,18.2049870404686,1.46188105097716,0.671087410204437,3.05661012316249,1.00646114393463,0.538118949022837,PCV20 +Netherlands.pre.PCV,16F,321,250924,2,4,0,adjusted_type_specific_negbin,0.0128074334113453,0.00439052763573673,0.028517302795545,0.244496875493983,0.148468880710923,0.406072957492,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,4.11118612504184,1.40935937107149,9.15405419736994,0.613554533305108,0.175888032724755,1.79062502052985,0.111186125041836,0.613554533305108,No PCV +Netherlands.pre.PCV,17F,321,250924,2,1,1,adjusted_type_specific_negbin,0.00707641681405198,0.0015627102307797,0.0191446694819052,0.244496875493983,0.148468880710923,0.406072957492,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,2.27152979731068,0.501629984080282,6.14543890369157,0.326285339670156,0.0647468186773989,1.1294434635792,1.27152979731068,0.673714660329844,PPV23 +Netherlands.pre.PCV,18C,321,250924,2,4,6,adjusted_type_specific_negbin,0.0156865666617946,0.00701536237239972,0.0311910695298461,0.244496875493983,0.148468880710923,0.406072957492,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,5.03538789843606,2.25193132154031,10.0123333190806,5.18578659188247,2.20165089508107,11.8028303320959,1.03538789843606,0.814213408117528,PCV7 +Netherlands.pre.PCV,19A,321,250924,2,9,5,adjusted_type_specific_negbin,0.0296345356899646,0.0159057040563653,0.0499849392906301,0.244496875493983,0.148468880710923,0.406072957492,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,9.51268595647863,5.10573100209328,16.0451655122922,5.57312333012678,2.72182528866139,11.1188835297234,0.512685956478634,0.573123330126782,PCV13 +Netherlands.pre.PCV,19F,321,250924,2,24,4,adjusted_type_specific_negbin,0.0747457824643673,0.0501766744948604,0.105975931340568,0.244496875493983,0.148468880710923,0.406072957492,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,23.9933961710619,16.1067125128502,34.0182739603223,5.86869702694815,3.14047087761543,10.8803994393091,0.00660382893808631,1.86869702694815,PCV7 +Netherlands.pre.PCV,21,321,250924,2,2,0,adjusted_type_specific_negbin,0.00768841692701829,0.00180238147858691,0.020711730086866,0.244496875493983,0.148468880710923,0.406072957492,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,2.46798183357287,0.578564454626399,6.648465357884,0.184452515201426,0.0353143594403696,0.682248115989878,0.467981833572872,0.184452515201426,No PCV +Netherlands.pre.PCV,22F,321,250924,2,2,0,adjusted_type_specific_negbin,0.00631612614398254,0.00145521935833374,0.0176656501801747,0.244496875493983,0.148468880710923,0.406072957492,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,2.0274764922184,0.467125414025132,5.67067370783607,0.786354129004725,0.17169819901825,2.4878761532107,0.0274764922183963,0.786354129004725,PCV15 +Netherlands.pre.PCV,23A,321,250924,2,1,1,adjusted_type_specific_negbin,0.00771329525089761,0.00182730366162598,0.0205526567662159,0.244496875493983,0.148468880710923,0.406072957492,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,2.47596777553813,0.586564475381941,6.59740282195529,0.14752508998882,0.0308328092180086,0.493980386042031,1.47596777553813,0.85247491001118,No PCV +Netherlands.pre.PCV,23B,321,250924,2,12,0,adjusted_type_specific_negbin,0.0365140239722534,0.0199295078517779,0.0603035394052611,0.244496875493983,0.148468880710923,0.406072957492,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,11.7210016950934,6.39737202042072,19.3574361490888,1.14620082291791,0.485449193109915,2.62075819611086,0.278998304906649,1.14620082291791,No PCV +Netherlands.pre.PCV,23F,321,250924,2,28,4,adjusted_type_specific_negbin,0.0859164681398703,0.0595109425025597,0.119045865731639,0.244496875493983,0.148468880710923,0.406072957492,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,27.5791862728984,19.1030125433217,38.213722899856,7.24059932133103,3.88290643670859,13.4227056276078,0.420813727101631,3.24059932133103,PCV7 +Netherlands.pre.PCV,24F,321,250924,2,1,0,adjusted_type_specific_negbin,0.00318246571100234,0.000444360441127316,0.0115247267054489,0.244496875493983,0.148468880710923,0.406072957492,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,1.02157149323175,0.142639701601868,3.69943727244911,0.848289902784225,0.111903796440745,3.45705552627546,0.0215714932317517,0.848289902784225,No PCV +Netherlands.pre.PCV,3,321,250924,2,3,1,adjusted_type_specific_negbin,0.00917452202979862,0.00294832082757701,0.0218682040248415,0.244496875493983,0.148468880710923,0.406072957492,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,2.94502157156536,0.946410985652219,7.01969349197411,2.2724829954666,0.710790692715024,6.06429347470695,0.0549784284346435,1.2724829954666,PCV13 +Netherlands.pre.PCV,33F,321,250924,2,6,1,adjusted_type_specific_negbin,0.0176816406581213,0.00769972062049573,0.0345974065931099,0.244496875493983,0.148468880710923,0.406072957492,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,5.67580665125693,2.47161031917913,11.1057675163883,2.86453193895408,1.08105750056773,7.14736568370496,0.324193348743066,1.86453193895408,PCV15 +Netherlands.pre.PCV,35B,321,250924,2,2,0,adjusted_type_specific_negbin,0.00788657867926363,0.00186487221916274,0.0211614731273898,0.244496875493983,0.148468880710923,0.406072957492,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,2.53159175604362,0.598623982351238,6.79283287389212,0.124812406631569,0.0238201206991325,0.452945327922284,0.531591756043624,0.124812406631569,No PCV +Netherlands.pre.PCV,38,321,250924,2,1,0,adjusted_type_specific_negbin,0.0040060077974773,0.0005302001301148,0.0141177415810771,0.244496875493983,0.148468880710923,0.406072957492,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,1.28592850299021,0.170194241766851,4.53179504752574,0.426278260016608,0.0524129241037805,1.76011277530334,0.285928502990212,0.426278260016608,No PCV +Netherlands.pre.PCV,4,321,250924,2,1,2,adjusted_type_specific_negbin,0.00643130063226835,0.00180242938263685,0.0168666377278766,0.244496875493983,0.148468880710923,0.406072957492,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,2.06444750295814,0.578579831826428,5.4141907106484,1.48328741314382,0.406457039459576,4.37486533594474,1.06444750295814,0.516712586856179,PCV7 +Netherlands.pre.PCV,6A,321,250924,2,25,5,adjusted_type_specific_negbin,0.0806865096049694,0.0550702176327875,0.113139675441844,0.244496875493983,0.148468880710923,0.406072957492,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,25.9003695831952,17.6775398601248,36.3178358168318,4.26862344070445,2.32565486223716,7.84186771889445,0.900369583195186,0.731376559295553,PCV13 +Netherlands.pre.PCV,6B,321,250924,2,43,16,adjusted_type_specific_negbin,0.137721510636554,0.103565762126393,0.177304636173151,0.244496875493983,0.148468880710923,0.406072957492,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,44.2086049143339,33.244609642572,56.9147882115814,12.5816601737788,7.28228840696266,21.9997179569774,1.20860491433386,3.41833982622117,PCV7 +Netherlands.pre.PCV,7F,321,250924,2,0,8,adjusted_type_specific_negbin,0.00515651227108511,0.00175381123378544,0.0131904884773705,0.244496875493983,0.148468880710923,0.406072957492,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,1.65524043901832,0.562973406045126,4.23414680123595,5.94663445022429,2.17734399965667,15.492985244003,1.65524043901832,2.05336554977571,PCV10 +Netherlands.pre.PCV,8,321,250924,2,0,2,adjusted_type_specific_negbin,0.00447000006242129,0.000938223714883544,0.0134071193475007,0.244496875493983,0.148468880710923,0.406072957492,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,1.43487002003723,0.301169812477617,4.30368531054771,1.03171032763211,0.20938436020891,3.46111858351351,1.43487002003723,0.968289672367887,PCV20 +Netherlands.pre.PCV,9N,321,250924,2,1,1,adjusted_type_specific_negbin,0.0066515906254103,0.00152504002327832,0.0186104365555746,0.244496875493983,0.148468880710923,0.406072957492,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,2.13516059075671,0.489537847472342,5.97395013433944,0.424267070268611,0.083969277247115,1.51812882863511,1.13516059075671,0.575732929731389,PPV23 +Netherlands.pre.PCV,9V,321,250924,2,6,8,adjusted_type_specific_negbin,0.0234083048884418,0.0118474678621903,0.0415081350181132,0.244496875493983,0.148468880710923,0.406072957492,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,7.51406586918981,3.8030371837631,13.3241113408143,5.82819375139611,2.66399209082381,12.517898474208,1.51406586918981,2.17180624860389,PCV7 +Portugal.pre.PCV,1,1170,2071223,2,1,15,adjusted_type_specific_negbin,0.00341556665102556,0.00153113680765339,0.00689212415173709,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.0172863329544385,0.00987005549069674,0.0314217272281422,3.54405372684984,2.48735345296771,5.1992340148223,3.99621298169991,1.79143006495446,8.06378525753239,8.04151400812596,3.73164495339083,17.2505877060304,2.99621298169991,6.95848599187404,PCV10 +Portugal.pre.PCV,10A,1170,2071223,2,19,2,adjusted_type_specific_negbin,0.0169634716329072,0.0107562059120431,0.0253028258958786,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,19.8472618105015,12.5847609170905,29.604306298178,1.66684767254528,0.798451962168857,3.36790672830004,0.847261810501465,0.333152327454724,PCV20 +Portugal.pre.PCV,11A,1170,2071223,2,42,0,adjusted_type_specific_negbin,0.0361853261741477,0.0265750629706525,0.047819248835153,0.0331720852733758,0.0203652157361025,0.0544492842088581,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,42.3368316237529,31.0928236756634,55.948521137129,0.332071803493441,0.142121603002,0.729393808915432,0.336831623752857,0.332071803493441,PCV20 +Portugal.pre.PCV,14,1170,2071223,2,52,12,adjusted_type_specific_negbin,0.0436333679865867,0.0331283877120724,0.0560897287079198,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,51.0510405443064,38.7602136231248,65.6249825882662,25.3058546951307,14.5869043233463,44.6825594333816,0.948959455693554,13.3058546951307,PCV7 +Portugal.pre.PCV,15A,1170,2071223,2,4,0,adjusted_type_specific_negbin,0.00379253141099661,0.00132831905231279,0.00839801906623149,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,4.43726175086603,1.55413329120597,9.82568230749085,0.214121834349051,0.0626548342044877,0.618714290848346,0.43726175086603,0.214121834349051,No PCV +Portugal.pre.PCV,15B/C,1170,2071223,2,33,1,adjusted_type_specific_negbin,0.0284420689016949,0.0200990446202307,0.0389218903677553,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,33.277220614983,23.51588220567,45.5386117302738,1.36030855563906,0.717941444441377,2.5491005352723,0.277220614983008,0.360308555639058,PCV20 +Portugal.pre.PCV,16F,1170,2071223,2,36,0,adjusted_type_specific_negbin,0.0303930352563818,0.0216759065563957,0.0410990140236084,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,35.5598512499667,25.3608106709829,48.0858464076218,1.64994062650472,0.721908013623479,3.58317337612982,0.440148750033259,1.64994062650472,No PCV +Portugal.pre.PCV,18A,1170,2071223,2,12,0,adjusted_type_specific_negbin,0.010509627524604,0.00570643609653842,0.0173765513184936,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000199167672918468,2.36758150914551e-05,0.00102580832813065,3.54405372684984,2.48735345296771,5.1992340148223,12.2962642037867,6.67653023294995,20.3305650426375,0.28613563733387,0.0325903974104606,1.52318944638764,0.296264203786681,0.28613563733387,No PCV +Portugal.pre.PCV,18C,1170,2071223,2,13,6,adjusted_type_specific_negbin,0.01224331176086,0.00729102114600991,0.0192348343553884,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,14.3246747602062,8.5304947408316,22.5047561958044,4.54896702671953,2.21391627242735,9.31250723182234,1.32467476020615,1.45103297328047,PCV7 +Portugal.pre.PCV,19A,1170,2071223,2,45,11,adjusted_type_specific_negbin,0.0396432198923501,0.0297609204945508,0.0515766627381935,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,46.3825672740496,34.8202769786244,60.3446954036864,8.410396230247,4.99782794166719,14.0975264879027,1.38256727404959,2.589603769753,PCV13 +Portugal.pre.PCV,19F,1170,2071223,2,93,1,adjusted_type_specific_negbin,0.0784092339017496,0.0640897989165494,0.0944563302079981,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,91.7388036650471,74.9850647323628,110.513906343358,6.91564441109942,3.94288529362714,12.1226559953577,1.26119633495293,5.91564441109942,PCV7 +Portugal.pre.PCV,20,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.00127792895623086,0.000181053810921379,0.00419508865128047,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,1.4951768787901,0.211832958778014,4.90825372199815,0.131056548814756,0.0141095102300863,0.675753315272083,1.4951768787901,0.868943451185244,PPV23 +Portugal.pre.PCV,21,1170,2071223,2,6,0,adjusted_type_specific_negbin,0.00555338520041963,0.00231714981544929,0.010860605070576,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,6.49746068449097,2.71106528407567,12.706907932574,0.150283171182585,0.0455752185315589,0.433054749464195,0.497460684490971,0.150283171182585,No PCV +Portugal.pre.PCV,22F,1170,2071223,2,8,0,adjusted_type_specific_negbin,0.00676961867960461,0.00319597744265638,0.0123682046074302,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,7.9204538551374,3.73929360790797,14.4707993906934,0.948157451327399,0.3694295476229,2.21337852806602,0.0795461448626025,0.948157451327399,PCV15 +Portugal.pre.PCV,23A,1170,2071223,2,11,0,adjusted_type_specific_negbin,0.00979202487719182,0.00519904607743942,0.0164015377737464,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,11.4566691063144,6.08288391060412,19.1897991952833,0.212601358980976,0.0834174483319506,0.497480342690671,0.456669106314425,0.212601358980976,No PCV +Portugal.pre.PCV,23B,1170,2071223,2,11,1,adjusted_type_specific_negbin,0.010449128751842,0.0057004687616663,0.0173028800129929,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,12.2254806396552,6.66954845114958,20.2443696152017,0.367118487854851,0.154205401735311,0.834075686356454,1.22548063965517,0.632881512145149,No PCV +Portugal.pre.PCV,23F,1170,2071223,2,70,13,adjusted_type_specific_negbin,0.0625351924249178,0.0497609526241378,0.0772000146128106,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,73.1661751371539,58.2203145702413,90.3240170969884,5.89194465836727,3.47233854031202,10.2110735753769,3.16617513715389,7.10805534163273,PCV7 +Portugal.pre.PCV,24F,1170,2071223,2,3,0,adjusted_type_specific_negbin,0.00259369671053759,0.000747871375246241,0.00633886230908801,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,3.03462515132898,0.875009509038102,7.41646890163297,0.773611412881904,0.194676893733651,2.40189752994759,0.0346251513289779,0.773611412881904,No PCV +Portugal.pre.PCV,3,1170,2071223,2,28,5,adjusted_type_specific_negbin,0.0239423989700064,0.0163699149014603,0.0336014091095604,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,28.0126067949075,19.1528004347086,39.3136486581857,6.65105754391672,3.61489887307468,12.5116336224559,0.0126067949075122,1.65105754391672,PCV13 +Portugal.pre.PCV,31,1170,2071223,2,7,1,adjusted_type_specific_negbin,0.00692219526522068,0.00330947069073307,0.0125623264903052,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,8.09896846030819,3.87208070815769,14.6979219936571,0.457376112589028,0.131694878761939,1.38920609742832,1.09896846030819,0.542623887410972,No PCV +Portugal.pre.PCV,33F,1170,2071223,2,4,1,adjusted_type_specific_negbin,0.00415266829268995,0.00158261037498958,0.00868462337479152,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,4.85862190244725,1.85165413873781,10.1610093485061,0.753834855762831,0.249389051190084,1.99234162266036,0.858621902447245,0.246165144237169,PCV15 +Portugal.pre.PCV,34,1170,2071223,2,18,0,adjusted_type_specific_negbin,0.0157585761592286,0.00963550999736618,0.0238568073622594,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,18.4375341062974,11.2735466969184,27.9124646138435,0.215246705608926,0.0452027777276092,0.764340736161723,0.437534106297448,0.215246705608926,No PCV +Portugal.pre.PCV,35F,1170,2071223,2,35,1,adjusted_type_specific_negbin,0.0307059588008297,0.0219825885581712,0.0414704690484884,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,35.9259717969708,25.7196286130603,48.5204487867315,0.627439440857279,0.253993791993465,1.45371915157109,0.925971796970757,0.372560559142721,No PCV +Portugal.pre.PCV,37,1170,2071223,2,9,0,adjusted_type_specific_negbin,0.00816880327630275,0.00403799325446595,0.0144034621010741,0.0331720852733758,0.0203652157361025,0.0544492842088581,8.82466692072548e-05,4.22185054013693e-06,0.000564483172719643,3.54405372684984,2.48735345296771,5.1992340148223,9.55749983327421,4.72445210772516,16.8520506582567,0.0967231668038644,0.00454208924624916,0.666136421789867,0.557499833274214,0.0967231668038644,No PCV +Portugal.pre.PCV,4,1170,2071223,2,4,0,adjusted_type_specific_negbin,0.00337777984453553,0.00115620923373863,0.00756328916922341,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,3.95200241810657,1.3527648034742,8.84904832799139,0.876888384204885,0.265790612590253,2.44560546906961,0.0479975818934273,0.876888384204885,PCV7 +Portugal.pre.PCV,5,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.000760237081491705,9.93666799153504e-05,0.00287523034788628,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00733836577997457,0.00296750469931036,0.0189575823678622,3.54405372684984,2.48735345296771,5.1992340148223,0.889477385345294,0.11625901550096,3.36401950702695,0.758724819866325,0.0983893389361582,3.21971558892143,0.889477385345294,0.241275180133675,PCV10 +Portugal.pre.PCV,6A,1170,2071223,2,64,3,adjusted_type_specific_negbin,0.0550699861314931,0.0432208764461013,0.0689317705779981,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,64.4318837738469,50.5684254419385,80.6501715762578,3.26983146822476,1.8613764740745,5.77392878141465,0.431883773846891,0.269831468224763,PCV13 +Portugal.pre.PCV,6B,1170,2071223,2,69,5,adjusted_type_specific_negbin,0.059245556346206,0.0468525043120495,0.0736119281463995,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,69.317300925061,54.8174300450979,86.1259559312874,6.07737813153239,3.49027116211078,10.5371033351066,0.317300925061033,1.07737813153239,PCV7 +Portugal.pre.PCV,6C,1170,2071223,2,14,0,adjusted_type_specific_negbin,0.012383447225734,0.00719717860803096,0.0197464918096894,0.0331720852733758,0.0203652157361025,0.0544492842088581,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,14.4886332541088,8.42069897139622,23.1033954173366,0.141695564345414,0.0488851500520863,0.379349158147665,0.488633254108752,0.141695564345414,No PCV +Portugal.pre.PCV,7F,1170,2071223,2,3,4,adjusted_type_specific_negbin,0.00320006923661987,0.0012502936539287,0.00685105723140618,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,3.74408100684525,1.46284357509658,8.01573696074523,4.11534297669137,1.56384942486123,10.0351706737689,0.744081006845247,0.115342976691365,PCV10 +Portugal.pre.PCV,8,1170,2071223,2,1,1,adjusted_type_specific_negbin,0.00182334726913238,0.000413657357559408,0.00501100319322925,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,2.13331630488488,0.483979108344507,5.86287373607822,0.47370073848592,0.0974158404620979,1.58561895931962,1.13331630488488,0.52629926151408,PCV20 +Portugal.pre.PCV,9L,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.000960801428643963,0.000103806182006641,0.00380486102814855,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00260956502335847,0.000181022012236223,0.0383407530403242,3.54405372684984,2.48735345296771,5.1992340148223,1.12413767151344,0.12145323294777,4.4516874029338,0.34178169880962,0.0175133840327634,2.97980211451461,1.12413767151344,0.65821830119038,No PCV +Portugal.pre.PCV,9N,1170,2071223,2,1,1,adjusted_type_specific_negbin,0.00210336593783077,0.000492056760202207,0.00567027318038584,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,2.460938147262,0.575706409436582,6.63421962105143,0.148518624917631,0.0292267668288103,0.55186165248384,1.460938147262,0.851481375082369,PPV23 +Portugal.pre.PCV,9V,1170,2071223,2,14,2,adjusted_type_specific_negbin,0.0119533026178793,0.0069061348840781,0.0189356807131834,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,13.9853640629188,8.08017781437138,22.1547464344246,3.34901609389631,1.51879014877195,7.19218304977147,0.0146359370812412,1.34901609389631,PCV7 +Portugal.pre.PCV,19C,1170,2071223,2,0,1,adjusted_type_specific_negbin,0.000596389599992263,2.1857180594556e-05,0.00316952113518536,0.0331720852733758,0.0203652157361025,0.0544492842088581,0.009902923624127,0.000200430251348706,0.474957262658767,3.54405372684984,2.48735345296771,5.1992340148223,0.697775831990948,0.0255729012956305,3.70833972816688,0.765435750745234,0.0265205847672187,6.4366086844432,0.697775831990948,0.234564249254766,No PCV +E.W.pre.PCV,10A,3752,3091000,1,1,0,adjusted_type_specific_negbin,0.000293985504243596,4.31024002437366e-05,0.00103732313316191,1.08128926008602,0.691234719461198,1.745949666522,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,1.10303361192197,0.1617202057145,3.8920363956235,0.706294853366974,0.10294061382229,2.74201296438946,0.103033611921971,0.706294853366974,PCV20 +E.W.pre.PCV,11A,3752,3091000,1,25,2,adjusted_type_specific_negbin,0.00691632960913654,0.00461255000182696,0.00991723814504512,1.08128926008602,0.691234719461198,1.745949666522,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,25.9500686934803,17.3062876068548,37.2094775202093,1.54665344742377,0.662222663766989,3.36086012037669,0.950068693480283,0.453346552576235,PCV20 +E.W.pre.PCV,14,3752,3091000,1,58,125,adjusted_type_specific_negbin,0.0152448299873454,0.011710142427306,0.0194239253338412,1.08128926008602,0.691234719461198,1.745949666522,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,57.19860211252,43.9364543872521,72.878567852572,215.717161989564,127.783046839087,371.556647518361,0.801397887479986,90.7171619895642,PCV7 +E.W.pre.PCV,15B/C,3752,3091000,1,15,8,adjusted_type_specific_negbin,0.00448869200754623,0.00277489468061871,0.00684340490813691,1.08128926008602,0.691234719461198,1.745949666522,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,16.8415724123135,10.4114048416814,25.6764552153297,5.23239924207623,2.7383706279363,9.78799411406461,1.84157241231346,2.76760075792377,PCV20 +E.W.pre.PCV,16F,3752,3091000,1,2,2,adjusted_type_specific_negbin,0.000877968381203219,0.000292178456941859,0.00204110453468291,1.08128926008602,0.691234719461198,1.745949666522,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,3.29413736627448,1.09625357044585,7.65822421413028,1.15250140831587,0.339878449281719,3.24210329300836,1.29413736627448,0.847498591684125,No PCV +E.W.pre.PCV,17F,3752,3091000,1,0,1,adjusted_type_specific_negbin,0.000321701768796527,4.58390248032581e-05,0.00111579053814904,1.08128926008602,0.691234719461198,1.745949666522,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,1.20702503652457,0.171988021061824,4.1864460991352,0.410844280905063,0.0543118996067128,1.64148759479139,1.20702503652457,0.589155719094937,PPV23 +E.W.pre.PCV,18B,3752,3091000,1,2,1,adjusted_type_specific_negbin,0.000526415111767568,0.000115199974869189,0.00152249484058227,1.08128926008602,0.691234719461198,1.745949666522,0.00124537383207727,0.000230254934727611,0.00649327559125252,3.54405372684984,2.48735345296771,5.1992340148223,1.97510949935192,0.432230305709197,5.71240064186469,2.11382170171523,0.3920190809834,9.90639311563956,0.0248905006480844,1.11382170171523,No PCV +E.W.pre.PCV,18C,3752,3091000,1,12,41,adjusted_type_specific_negbin,0.00363826700646453,0.00215544273846456,0.00573270457962501,1.08128926008602,0.691234719461198,1.745949666522,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,13.6507778082549,8.08722115471902,21.5091075827531,32.740299081257,17.271343532168,64.9558909696708,1.6507778082549,8.25970091874296,PCV7 +E.W.pre.PCV,19A,3752,3091000,1,18,20,adjusted_type_specific_negbin,0.00482700041073185,0.00306094596515939,0.00727812507423586,1.08128926008602,0.691234719461198,1.745949666522,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,18.1109055410659,11.484669261278,27.3075252785329,24.8635510425738,13.8903976880441,44.9704919068638,0.1109055410659,4.86355104257376,PCV13 +E.W.pre.PCV,19F,3752,3091000,1,92,52,adjusted_type_specific_negbin,0.0247055941808576,0.0201078781565272,0.0299105343873414,1.08128926008602,0.691234719461198,1.745949666522,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,92.6953893665779,75.4447588432901,112.224325021305,52.880644789935,32.2980024681338,89.4607004718921,0.695389366577899,0.880644789935033,PCV7 +E.W.pre.PCV,20,3752,3091000,1,0,1,adjusted_type_specific_negbin,0.000254948125847697,3.32127587479695e-05,0.000966025192442894,1.08128926008602,0.691234719461198,1.745949666522,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,0.95656536818056,0.124614270822382,3.62452652204574,0.640072470165211,0.0798259799122393,2.95235821221262,0.95656536818056,0.359927529834789,PPV23 +E.W.pre.PCV,21,3752,3091000,1,4,0,adjusted_type_specific_negbin,0.00108619526934598,0.000372455370152276,0.00240435264557134,1.08128926008602,0.691234719461198,1.745949666522,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,4.07540465058612,1.39745254881134,9.02113112618367,0.717629491899525,0.201560090508414,2.11779135158157,0.0754046505861234,0.717629491899525,No PCV +E.W.pre.PCV,22F,3752,3091000,1,11,9,adjusted_type_specific_negbin,0.00304586284254906,0.00172555664710952,0.00501026901461524,1.08128926008602,0.691234719461198,1.745949666522,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,11.4280773852441,6.47428853995492,18.7985293428364,10.3951514190314,5.03299808035156,21.2287525018317,0.42807738524408,1.39515141903144,PCV15 +E.W.pre.PCV,23A,3752,3091000,1,9,2,adjusted_type_specific_negbin,0.00268055790239688,0.00138674691490341,0.00460595164147381,1.08128926008602,0.691234719461198,1.745949666522,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,10.0574532497931,5.2030744247176,17.2815305588097,1.41497272269691,0.582697535629029,3.20048101963686,1.05745324979311,0.585027277303091,No PCV +E.W.pre.PCV,23F,3752,3091000,1,88,43,adjusted_type_specific_negbin,0.0234744980623596,0.019030865831866,0.0284513086883358,1.08128926008602,0.691234719461198,1.745949666522,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,88.0763167299731,71.4038086011612,106.749310198636,54.1134462523875,32.0576405470778,93.7151652618151,0.0763167299730867,11.1134462523875,PCV7 +E.W.pre.PCV,27,3752,3091000,1,1,1,adjusted_type_specific_negbin,0.00019856386985553,2.98035203648015e-05,0.000803267108619067,1.08128926008602,0.691234719461198,1.745949666522,0.00445332639932121,0.00109948577435022,0.0190137059440571,3.54405372684984,2.48735345296771,5.1992340148223,0.745011639697949,0.111822808408735,3.01385819153874,2.84328910932157,0.523376611855165,13.1125231460566,0.254988360302051,1.84328910932157,No PCV +E.W.pre.PCV,3,3752,3091000,1,4,6,adjusted_type_specific_negbin,0.00113053208220221,0.000487587264881729,0.00235621548545716,1.08128926008602,0.691234719461198,1.745949666522,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,4.24175637242269,1.82942741783625,8.84052050143526,7.68058132293276,3.24253364237864,17.7213708173542,0.24175637242269,1.68058132293276,PCV13 +E.W.pre.PCV,31,3752,3091000,1,1,0,adjusted_type_specific_negbin,0.000321213426713478,4.6175436456858e-05,0.00113103743981887,1.08128926008602,0.691234719461198,1.745949666522,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,1.20519277702897,0.173250237586131,4.24365247420038,0.513956572691242,0.0661260018239554,2.31930552236775,0.205192777028971,0.513956572691242,No PCV +E.W.pre.PCV,35B,3752,3091000,1,4,1,adjusted_type_specific_negbin,0.00133226964838909,0.000509708727455139,0.0027957140006463,1.08128926008602,0.691234719461198,1.745949666522,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,4.99867572075587,1.91242714541168,10.4895189304249,0.574465305383334,0.173984076556691,1.62579138495194,0.998675720755869,0.425534694616666,No PCV +E.W.pre.PCV,35F,3752,3091000,1,15,1,adjusted_type_specific_negbin,0.00401364056370271,0.00234560736124318,0.00630649719414018,1.08128926008602,0.691234719461198,1.745949666522,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,15.0591793950126,8.80071881938442,23.6619774724139,1.98698884148833,0.77378289150596,4.83771587309795,0.059179395012583,0.986988841488329,No PCV +E.W.pre.PCV,38,3752,3091000,1,1,3,adjusted_type_specific_negbin,0.000645669963957526,0.00019353179085287,0.00160884268449805,1.08128926008602,0.691234719461198,1.745949666522,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,2.42255370476864,0.726131279279967,6.0363777522367,1.87112887995274,0.545064656409585,5.45296739341326,1.42255370476864,1.12887112004726,No PCV +E.W.pre.PCV,4,3752,3091000,1,0,10,adjusted_type_specific_negbin,0.000783983818977441,0.000307192950269335,0.0017158370570694,1.08128926008602,0.691234719461198,1.745949666522,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,2.94150728880336,1.15258794941055,6.43782063812438,4.94538930170775,2.06645097842554,11.4309882495211,2.94150728880336,5.05461069829225,PCV7 +E.W.pre.PCV,6A,3752,3091000,1,82,16,adjusted_type_specific_negbin,0.0216496304116515,0.0173229929772654,0.0264572118186717,1.08128926008602,0.691234719461198,1.745949666522,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,81.2294133045163,64.9958696506996,99.2674587436561,31.3231457649565,18.452461157375,54.1821363983117,0.770586695483658,15.3231457649565,PCV13 +E.W.pre.PCV,6B,3752,3091000,1,186,64,adjusted_type_specific_negbin,0.0492992061745526,0.0427556318151026,0.0564111922833582,1.08128926008602,0.691234719461198,1.745949666522,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,184.970621566921,160.419130570265,211.65479344716,123.34975192862,75.3127612837145,207.571505292915,1.02937843307873,59.3497519286195,PCV7 +E.W.pre.PCV,7F,3752,3091000,1,2,10,adjusted_type_specific_negbin,0.000502459145720369,0.000172672334254878,0.00128962640686992,1.08128926008602,0.691234719461198,1.745949666522,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,1.88522671474282,0.647866598124301,4.83867827857596,15.6955021111723,5.6758200305382,43.8446574659692,0.114773285257176,5.69550211117234,PCV10 +E.W.pre.PCV,8,3752,3091000,1,0,8,adjusted_type_specific_negbin,0.000667153610264818,0.000239098273789035,0.00156980334265916,1.08128926008602,0.691234719461198,1.745949666522,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,2.5031603457136,0.897096723256461,5.88990214165716,4.21015101069859,1.62930196284433,10.4788206204865,2.5031603457136,3.78984898930141,PCV20 +E.W.pre.PCV,9N,3752,3091000,1,4,6,adjusted_type_specific_negbin,0.00170247110094929,0.000788721466778485,0.00320696357368255,1.08128926008602,0.691234719461198,1.745949666522,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,6.38767157076172,2.95928294335287,12.0325273284569,2.94618088708277,1.1529320708741,7.13702789582504,2.38767157076172,3.05381911291723,PPV23 +E.W.pre.PCV,9V,3752,3091000,1,11,28,adjusted_type_specific_negbin,0.0033456729526348,0.00194723333924569,0.0053679512738081,1.08128926008602,0.691234719461198,1.745949666522,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,12.5529649182858,7.30601948884982,20.140553179328,22.7479904755346,11.7007710737224,46.0703951199993,1.55296491828578,5.25200952446544,PCV7 +France.post.PCV13,10A,1212,842076,2,11,14,adjusted_type_specific_negbin,0.00996653429839838,0.00572492492483053,0.0160515371723477,1.05731919431183,0.666742682001165,1.69598304908418,0.000717783022245954,0.000402801751829467,0.00128853269468596,3.54405372684984,2.48735345296771,5.1992340148223,12.0794395696588,6.9386090088946,19.4544630528854,12.5996950772679,6.35408250581278,24.9793948747677,1.07943956965883,1.40030492273212,PCV20 +France.post.PCV13,10B,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000853844223346744,0.000105879246143142,0.00319722737787738,1.05731919431183,0.666742682001165,1.69598304908418,0.000502204985915827,8.47222594103277e-05,0.00253825696624574,3.54405372684984,2.48735345296771,5.1992340148223,1.03485919869625,0.128325646325489,3.87503958198738,0.728383399843164,0.0702926382049728,4.18668507891213,0.0348591986962541,0.728383399843164,No PCV +France.post.PCV13,11A,1212,842076,2,13,2,adjusted_type_specific_negbin,0.0116117293388048,0.00673596897653034,0.0184809359468514,1.05731919431183,0.666742682001165,1.69598304908418,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,14.0734159586314,8.16399439955477,22.3988943675839,1.37937188470863,0.562681548696247,3.10872247517278,1.07341595863138,0.620628115291368,PCV20 +France.post.PCV13,11B,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000568116370377506,1.93943199191228e-05,0.00306276196956594,1.05731919431183,0.666742682001165,1.69598304908418,0.000790667125874541,1.59854838393407e-05,0.0398621101307321,3.54405372684984,2.48735345296771,5.1992340148223,0.688557040897538,0.0235059157419768,3.71206750711392,0.771840918769744,0.0238028520067867,6.55823608149405,0.688557040897538,0.228159081230256,No PCV +France.post.PCV13,11F,1212,842076,2,1,0,adjusted_type_specific_negbin,0.00125038556811508,0.000162439480671793,0.00429780228014144,1.05731919431183,0.666742682001165,1.69598304908418,1.7473223411487e-05,1.15709944830945e-06,0.00121250191153361,3.54405372684984,2.48735345296771,5.1992340148223,1.51546730855547,0.196876650574213,5.20893636353142,0.0410008707778724,0.00129020677998543,1.87029009583379,0.515467308555474,0.0410008707778724,No PCV +France.post.PCV13,12F,1212,842076,2,0,16,adjusted_type_specific_negbin,0.00126562771697058,0.00041407229353861,0.0033692385181249,1.05731919431183,0.666742682001165,1.69598304908418,0.00604172772796168,0.00276457252642332,0.013992691352501,3.54405372684984,2.48735345296771,5.1992340148223,1.53394079296834,0.501855619768796,4.08351708396738,13.3603202090101,5.43948084895063,35.2718878402202,1.53394079296834,2.63967979098988,PCV20 +France.post.PCV13,14,1212,842076,2,2,2,adjusted_type_specific_negbin,0.000961327663812751,0.000246403302419794,0.00313926159378299,1.05731919431183,0.666742682001165,1.69598304908418,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,1.16512912854105,0.29864080253279,3.80478505166498,7.21841711390783,1.86756551216505,24.2395223335325,0.834870871458946,5.21841711390783,PCV7 +France.post.PCV13,15A,1212,842076,2,14,13,adjusted_type_specific_negbin,0.0129173388101282,0.00790713992471619,0.0200527196829222,1.05731919431183,0.666742682001165,1.69598304908418,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,15.6558146378754,9.58345358875602,24.3038962557017,9.52628672091863,4.83398011854134,19.3244436273066,1.65581463787543,3.47371327908137,No PCV +France.post.PCV13,15B/C,1212,842076,2,22,15,adjusted_type_specific_negbin,0.0193447051271067,0.0128834146884727,0.0276482357805766,1.05731919431183,0.666742682001165,1.69598304908418,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,23.4457826140533,15.6146986024289,33.5096617660589,11.9710560645378,6.72420647114024,21.7448745445865,1.44578261405334,3.02894393546217,PCV20 +France.post.PCV13,15F,1212,842076,2,0,2,adjusted_type_specific_negbin,0.00159242297631436,0.00034101405935202,0.00466074934421521,1.05731919431183,0.666742682001165,1.69598304908418,0.000169416469056684,1.99360904401105e-05,0.000839805104163891,3.54405372684984,2.48735345296771,5.1992340148223,1.930016647293,0.413309039934648,5.64882820518883,0.46193304324566,0.0465957424843213,2.3957048132124,1.930016647293,1.53806695675434,No PCV +France.post.PCV13,16F,1212,842076,2,3,1,adjusted_type_specific_negbin,0.00259845476741732,0.000835190773677887,0.00611220457414949,1.05731919431183,0.666742682001165,1.69598304908418,0.000397582429973281,0.000188448551879674,0.000797987375007872,3.54405372684984,2.48735345296771,5.1992340148223,3.14932717810979,1.0122512176976,7.40799194386918,1.81713810110359,0.52566704056044,5.06751416639283,0.149327178109795,0.817138101103593,No PCV +France.post.PCV13,17F,1212,842076,2,8,3,adjusted_type_specific_negbin,0.00665902021799308,0.0032504248570175,0.0119572743547029,1.05731919431183,0.666742682001165,1.69598304908418,0.000385129667120494,0.00017472697765225,0.000808460730390785,3.54405372684984,2.48735345296771,5.1992340148223,8.07073250420762,3.93951492670521,14.4922165178999,4.49108059518648,1.77892123223154,10.8904378409533,0.0707325042076192,1.49108059518648,PPV23 +France.post.PCV13,19A,1212,842076,2,8,16,adjusted_type_specific_negbin,0.00685571854477265,0.00362566736106209,0.0120781808086346,1.05731919431183,0.666742682001165,1.69598304908418,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,8.30913087626446,4.39430884160725,14.6387551400652,18.7984202195886,9.40565557282245,37.4646235340925,0.309130876264458,2.79842021958861,PCV13 +France.post.PCV13,19F,1212,842076,2,6,7,adjusted_type_specific_negbin,0.00569604440556746,0.00284489028700972,0.0104286367456593,1.05731919431183,0.666742682001165,1.69598304908418,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,6.90360581954776,3.44800702785578,12.6395077357391,6.46579206589962,3.00152417438031,13.5023654928172,0.903605819547764,0.534207934100381,PCV7 +France.post.PCV13,2,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000240878439657141,1.26256784852958e-05,0.00181518019323977,1.05731919431183,0.666742682001165,1.69598304908418,0.0040320840401038,0.000264894385084091,0.0500576564904172,3.54405372684984,2.48735345296771,5.1992340148223,0.291944668864455,0.0153023223241785,2.1999983942066,1.57259159185787,0.159727217822226,9.76533826656853,0.291944668864455,0.572591591857875,PPV23 +France.post.PCV13,20,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000748992004463649,9.66423474374739e-05,0.00286887464649427,1.05731919431183,0.666742682001165,1.69598304908418,0.000773292611718912,0.000204023972119869,0.00255784196731255,3.54405372684984,2.48735345296771,5.1992340148223,0.907778309409942,0.117130525094218,3.47707607155105,0.995273194266203,0.116979624615355,4.99164813884133,0.0922216905900579,0.995273194266203,PPV23 +France.post.PCV13,21,1212,842076,2,3,3,adjusted_type_specific_negbin,0.00395135157872653,0.00160094742767365,0.00815746475104654,1.05731919431183,0.666742682001165,1.69598304908418,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,4.78903811341655,1.94034828234046,9.8868472782684,1.39607212970451,0.470680373752009,3.60467491952629,1.78903811341655,1.60392787029549,No PCV +France.post.PCV13,22F,1212,842076,2,6,9,adjusted_type_specific_negbin,0.00544201113462158,0.00264818002644309,0.0100297023465974,1.05731919431183,0.666742682001165,1.69598304908418,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,6.59571749516136,3.20959419204903,12.1559992440761,9.79800472399824,4.48712378476755,21.4370191387854,0.59571749516136,0.798004723998243,PCV15 +France.post.PCV13,23A,1212,842076,2,9,4,adjusted_type_specific_negbin,0.00872026614352019,0.00469601693747518,0.014664122113333,1.05731919431183,0.666742682001165,1.69598304908418,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,10.5689625659465,5.69157252821992,17.7729160013597,2.45412610753901,1.07472073205118,5.34276905199714,1.56896256594647,1.54587389246099,No PCV +France.post.PCV13,23B,1212,842076,2,15,2,adjusted_type_specific_negbin,0.0118153295883069,0.00697249824252332,0.0185443696169522,1.05731919431183,0.666742682001165,1.69598304908418,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,14.3201794610279,8.45066786993826,22.4757759757461,5.39819150349777,2.5200334957762,11.4626829453768,0.679820538972081,3.39819150349777,No PCV +France.post.PCV13,24A,1212,842076,2,1,1,adjusted_type_specific_negbin,0.00137993796712575,0.000198804082169833,0.00467845341891006,1.05731919431183,0.666742682001165,1.69598304908418,0.000311987172256277,1.02706243870991e-05,0.0056545629114863,3.54405372684984,2.48735345296771,5.1992340148223,1.6724848161564,0.240950547589838,5.67028554371899,0.764309613374866,0.0298546308032454,6.55395606770849,0.672484816156404,0.235690386625134,No PCV +France.post.PCV13,24F,1212,842076,2,6,36,adjusted_type_specific_negbin,0.00671221718178369,0.00350161238665176,0.0117992878594184,1.05731919431183,0.666742682001165,1.69598304908418,0.00219490951686074,0.00103249583784539,0.00475359918251703,3.54405372684984,2.48735345296771,5.1992340148223,8.13520722432183,4.24395421262194,14.300736885615,25.8812908234432,12.6631464007987,56.5390877107592,2.13520722432183,10.1187091765568,No PCV +France.post.PCV13,25A,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000544007635701689,6.57196600139326e-05,0.00230467662225803,1.05731919431183,0.666742682001165,1.69598304908418,0.00163929978568756,0.000579341956760081,0.00489291543751703,3.54405372684984,2.48735345296771,5.1992340148223,0.659337254470446,0.0796522279368863,2.79326806617673,1.56564404777746,0.19801298802385,7.47309834378538,0.340662745529554,1.56564404777746,No PCV +France.post.PCV13,29,1212,842076,2,1,1,adjusted_type_specific_negbin,0.00191508537846152,0.000435825941577375,0.00533775490085073,1.05731919431183,0.666742682001165,1.69598304908418,6.4477890005963e-05,3.10034323663527e-06,0.000486340435351969,3.54405372684984,2.48735345296771,5.1992340148223,2.32108347869536,0.528221041191778,6.46935893983108,0.208595295406702,0.00931151006968732,1.62175402130082,1.32108347869536,0.791404704593298,No PCV +France.post.PCV13,3,1212,842076,2,1,5,adjusted_type_specific_negbin,0.00144805365833036,0.000474908567306606,0.00379165111299875,1.05731919431183,0.666742682001165,1.69598304908418,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,1.75504103389639,0.575589183575607,4.59548114895448,5.19571571428515,1.77450456076749,14.367306000604,0.755041033896392,0.195715714285146,PCV13 +France.post.PCV13,31,1212,842076,2,2,1,adjusted_type_specific_negbin,0.00188459957176742,0.000492454436297173,0.00494825205777846,1.05731919431183,0.666742682001165,1.69598304908418,0.00048954548673512,0.000169207621326834,0.00127226840209249,3.54405372684984,2.48735345296771,5.1992340148223,2.28413468098211,0.596854776792173,5.99728149402749,1.59413786047175,0.374287946997478,5.4096656510676,0.284134680982109,0.594137860471751,No PCV +France.post.PCV13,33F,1212,842076,2,3,6,adjusted_type_specific_negbin,0.00289633928045678,0.00116316451988579,0.00625415677812643,1.05731919431183,0.666742682001165,1.69598304908418,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,3.51036320791361,1.40975539810158,7.58003801508923,6.8229691579921,2.69864486802711,16.827801946081,0.510363207913613,0.822969157992102,PCV15 +France.post.PCV13,34,1212,842076,2,1,0,adjusted_type_specific_negbin,0.0011980081737578,0.00017266786324225,0.00408336076207171,1.05731919431183,0.666742682001165,1.69598304908418,0.000100648926332244,2.23088987087083e-05,0.000327303393776831,3.54405372684984,2.48735345296771,5.1992340148223,1.45198590659446,0.209273450249606,4.94903324363091,0.201231859528485,0.0199893129235287,1.10085355764902,0.451985906594459,0.201231859528485,No PCV +France.post.PCV13,35B,1212,842076,2,7,4,adjusted_type_specific_negbin,0.00754371714932358,0.00389318360236566,0.0130863904704262,1.05731919431183,0.666742682001165,1.69598304908418,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,9.14298518498018,4.71853852606718,15.8607052501565,1.73248558094546,0.673316800858014,4.11838581718525,2.14298518498018,2.26751441905454,No PCV +France.post.PCV13,35F,1212,842076,2,4,2,adjusted_type_specific_negbin,0.00434097191240248,0.00179287271187336,0.00881353246450871,1.05731919431183,0.666742682001165,1.69598304908418,0.00014978286464869,6.39234148174072e-05,0.000327740906379591,3.54405372684984,2.48735345296771,5.1992340148223,5.26125795783181,2.17296172679052,10.6820013469846,1.14261339326237,0.371344440686449,3.06807175723947,1.26125795783181,0.857386606737627,No PCV +France.post.PCV13,38,1212,842076,2,0,5,adjusted_type_specific_negbin,0.00172503347597056,0.000546289566636431,0.00439805094283151,1.05731919431183,0.666742682001165,1.69598304908418,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,2.09074057287632,0.662102954763354,5.33043774271179,2.66331091829761,0.868873034707315,7.29104170561441,2.09074057287632,2.33668908170239,No PCV +France.post.PCV13,4,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000410321071045063,5.11700331655835e-05,0.00176390232703264,1.05731919431183,0.666742682001165,1.69598304908418,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,0.497309138106616,0.0620180801966872,2.13784962036355,1.40504001232441,0.184518827880293,5.90437110866873,0.497309138106616,0.405040012324408,PCV7 +France.post.PCV13,6A,1212,842076,2,0,1,adjusted_type_specific_negbin,0.00083107544832906,0.000115492696524348,0.00300947408099201,1.05731919431183,0.666742682001165,1.69598304908418,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,1.00726344337482,0.13997714818751,3.64748258616231,0.638778219499963,0.0868241252303912,2.46132664325605,1.00726344337482,0.361221780500037,PCV13 +France.post.PCV13,6B,1212,842076,2,2,0,adjusted_type_specific_negbin,0.00129873960423765,0.000274560323818307,0.00396764880540604,1.05731919431183,0.666742682001165,1.69598304908418,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,1.57407240033603,0.332767112467788,4.80879035215212,1.71198452781323,0.36064250874999,5.66461027588585,0.425927599663967,1.71198452781323,PCV7 +France.post.PCV13,6C,1212,842076,2,6,1,adjusted_type_specific_negbin,0.00559015100580058,0.00247074974465428,0.0106298766925143,1.05731919431183,0.666742682001165,1.69598304908418,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,6.7752630190303,2.99454869052099,12.8834105513273,0.818866892622571,0.26145159875363,2.285812646589,0.775263019030302,0.181133107377429,No PCV +France.post.PCV13,7C,1212,842076,2,0,1,adjusted_type_specific_negbin,0.000841837038664305,0.000111106695779298,0.00309603211332581,1.05731919431183,0.666742682001165,1.69598304908418,0.000393012283852677,0.00011306744230165,0.00121318243232636,3.54405372684984,2.48735345296771,5.1992340148223,1.02030649086114,0.134661315284509,3.75239092135088,0.576264009600021,0.0688926374928399,2.60870711817603,1.02030649086114,0.423735990399979,No PCV +France.post.PCV13,7F,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000188854071238253,1.9908947838352e-05,0.00114906192584734,1.05731919431183,0.666742682001165,1.69598304908418,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,0.228891134340762,0.0241296447800827,1.39266305412698,3.18296469505186,0.351751538848133,19.8029732432899,0.771108865659238,3.18296469505186,PCV10 +France.post.PCV13,9N,1212,842076,2,1,0,adjusted_type_specific_negbin,0.000851749244298076,0.00011585499359654,0.00313805298172492,1.05731919431183,0.666742682001165,1.69598304908418,0.000523851634940353,0.000215172253573282,0.00123832773062787,3.54405372684984,2.48735345296771,5.1992340148223,1.03232008408927,0.140416252239006,3.8033202138506,0.783561586935712,0.104095639964387,3.27295858495132,0.0323200840892683,0.783561586935712,PPV23 +Atlanta.post.PCV7,11A,451,298831,1,10,0,adjusted_type_specific_negbin,0.0227865275026288,0.0117152269812652,0.0390511599095501,0.875380655148894,0.461657827922813,1.67723497095231,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,10.2767239036856,5.28356736855062,17.6120731192071,0.394860664014816,0.135229274045759,1.04857975861654,0.276723903685596,0.394860664014816,PCV20 +Atlanta.post.PCV7,12F,451,298831,1,0,1,adjusted_type_specific_negbin,0.00096098525578856,0.000111933125570157,0.00440140219748866,0.875380655148894,0.461657827922813,1.67723497095231,0.00604172772796168,0.00276457252642332,0.013992691352501,3.54405372684984,2.48735345296771,5.1992340148223,0.433404350360641,0.0504818396321409,1.98503239106739,1.50649919684395,0.19725609227927,6.96154344619661,0.433404350360641,0.506499196843945,PCV20 +Atlanta.post.PCV7,13,451,298831,1,0,1,adjusted_type_specific_negbin,0.00256575252413926,0.000361596707486027,0.00919295081420749,0.875380655148894,0.461657827922813,1.67723497095231,0.000646064239496631,0.000179626011284756,0.00211440991216995,3.54405372684984,2.48735345296771,5.1992340148223,1.15715438838681,0.163080115076198,4.14602081720758,0.42682846095324,0.0488540296258549,2.03438843163764,1.15715438838681,0.57317153904676,No PCV +Atlanta.post.PCV7,15A,451,298831,1,4,0,adjusted_type_specific_negbin,0.00869241596936591,0.00303299948755142,0.0193562751370707,0.875380655148894,0.461657827922813,1.67723497095231,0.000417194343144857,0.000219550995865584,0.0007945252585372,3.54405372684984,2.48735345296771,5.1992340148223,3.92027960218403,1.36788276888569,8.7296800868189,0.935874902214103,0.275736162213008,2.75889553791271,0.0797203978159726,0.935874902214103,No PCV +Atlanta.post.PCV7,15B/C,451,298831,1,8,3,adjusted_type_specific_negbin,0.0207122901575845,0.0107049457029805,0.0357066139006107,0.875380655148894,0.461657827922813,1.67723497095231,0.000349872656208534,0.000205374575481143,0.000590023394425282,3.54405372684984,2.48735345296771,5.1992340148223,9.34124286107059,4.82793051204422,16.1036828691754,1.88109570807459,0.788495265109756,4.24482424673227,1.34124286107059,1.11890429192541,PCV20 +Atlanta.post.PCV7,19A,451,298831,1,29,23,adjusted_type_specific_negbin,0.0651088253304676,0.0455396362773086,0.0893523577026695,0.875380655148894,0.461657827922813,1.67723497095231,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,29.3640802240409,20.5383759610662,40.2979133239039,26.1449318168894,13.7500701644612,51.2544550577149,0.364080224040883,3.14493181688938,PCV13 +Atlanta.post.PCV7,19F,451,298831,1,1,0,adjusted_type_specific_negbin,0.00279535652992557,0.000410146263004468,0.00970493342001989,0.875380655148894,0.461657827922813,1.67723497095231,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,1.26070579499643,0.184975964615015,4.37692497242897,0.463672622374377,0.0656766334655548,1.83368992454263,0.260705794996434,0.463672622374377,PCV7 +Atlanta.post.PCV7,21,451,298831,1,3,2,adjusted_type_specific_negbin,0.0107947715291889,0.00417741255616466,0.0221825489250718,0.875380655148894,0.461657827922813,1.67723497095231,0.000200088645461598,8.67637704801456e-05,0.000436853234329197,3.54405372684984,2.48735345296771,5.1992340148223,4.86844195966419,1.88401306283026,10.0043295652074,0.555869743052022,0.158578584531145,1.62345501429558,1.86844195966419,1.44413025694798,No PCV +Atlanta.post.PCV7,22F,451,298831,1,0,2,adjusted_type_specific_negbin,0.00342516665532561,0.000734939178038692,0.0101955151883922,0.875380655148894,0.461657827922813,1.67723497095231,0.0010269142195402,0.000574607551073163,0.00184567780557173,3.54405372684984,2.48735345296771,5.1992340148223,1.54475016155185,0.33145756929545,4.5981773499649,0.907810343692804,0.187897790529157,3.07122773267638,1.54475016155185,1.0921896563072,PCV15 +Atlanta.post.PCV7,23A,451,298831,1,10,0,adjusted_type_specific_negbin,0.0219206670744751,0.0111882084618868,0.0381065613323348,0.875380655148894,0.461657827922813,1.67723497095231,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,9.88622085058826,5.04588201631096,17.186059160883,0.906081673275608,0.324566168269015,2.30728233571759,0.113779149411743,0.906081673275608,No PCV +Atlanta.post.PCV7,23B,451,298831,1,10,1,adjusted_type_specific_negbin,0.0227810403445926,0.0119568883539467,0.0387014326339959,0.875380655148894,0.461657827922813,1.67723497095231,0.00025888640659992,0.000137713928235595,0.000474339785205248,3.54405372684984,2.48735345296771,5.1992340148223,10.2742491954113,5.39255664762998,17.4543461179322,1.52884445619367,0.599387921655465,3.67603103538135,0.274249195411272,0.528844456193671,No PCV +Atlanta.post.PCV7,3,451,298831,1,0,1,adjusted_type_specific_negbin,0.00173283216165413,0.000231724933564398,0.00651205306139536,0.875380655148894,0.461657827922813,1.67723497095231,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,0.781507304906012,0.104507945037543,2.93693593068931,0.918568858613872,0.12368957817022,3.69935022763736,0.781507304906012,0.0814311413861284,PCV13 +Atlanta.post.PCV7,33F,451,298831,1,5,6,adjusted_type_specific_negbin,0.0138973185748964,0.00651701593927203,0.0261052121185361,0.875380655148894,0.461657827922813,1.67723497095231,0.00134021075506889,0.000695667738152149,0.0025832656626784,3.54405372684984,2.48735345296771,5.1992340148223,6.26769067727828,2.93917418861168,11.7734506654598,4.79203836900709,1.98149011860167,11.4661723748666,1.26769067727828,1.20796163099291,PCV15 +Atlanta.post.PCV7,35B,451,298831,1,14,1,adjusted_type_specific_negbin,0.0321920899786686,0.0186992976029014,0.0509977092693685,0.875380655148894,0.461657827922813,1.67723497095231,0.000130542930938921,5.6869794515505e-05,0.000283470660815841,3.54405372684984,2.48735345296771,5.1992340148223,14.5186325803795,8.43338321890852,22.9999668804852,1.09028997345328,0.388988861898641,2.84237174383781,0.518632580379538,0.0902899734532827,No PCV +Atlanta.post.PCV7,38,451,298831,1,0,2,adjusted_type_specific_negbin,0.00358256036415158,0.000785822340377074,0.0104581612402584,0.875380655148894,0.461657827922813,1.67723497095231,0.000879697208331091,0.000380234437153394,0.00197471506733782,3.54405372684984,2.48735345296771,5.1992340148223,1.61573472423236,0.35440587551006,4.71663071935655,0.811503722723302,0.163196916241591,2.8967665300327,1.61573472423236,1.1884962772767,No PCV +Atlanta.post.PCV7,6C,451,298831,1,23,0,adjusted_type_specific_negbin,0.0505455171752416,0.0330804853483824,0.0727733974882414,0.875380655148894,0.461657827922813,1.67723497095231,8.39297436563988e-05,3.31729844075944e-05,0.000197506511283946,3.54405372684984,2.48735345296771,5.1992340148223,22.796028246034,14.9192988921205,32.8208022671969,1.10048357287917,0.381272841093749,2.94700492174438,0.203971753966048,1.10048357287917,No PCV +Atlanta.post.PCV7,7F,451,298831,1,0,4,adjusted_type_specific_negbin,0.0017199607057138,0.000423712976384162,0.00568464566811933,0.875380655148894,0.461657827922813,1.67723497095231,0.00949870839542005,0.00558063522272554,0.0165677856373084,3.54405372684984,2.48735345296771,5.1992340148223,0.775702278276925,0.191094552349257,2.56377519632182,4.22559486397408,1.17180722314559,13.984440779474,0.775702278276925,0.22559486397408,PCV10 +Atlanta.pre.PCV,11A,231,204680,1,5,0,adjusted_type_specific_negbin,0.0217429110770419,0.00827411015815152,0.0449658335796084,2.44771166883747,1.37121545978538,4.50865449346866,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,5.02261245879667,1.911319446533,10.3871075568895,0.715577026765314,0.216003003085714,2.0684108969121,0.0226124587966687,0.715577026765314,PCV20 +Atlanta.pre.PCV,14,231,204680,1,3,67,adjusted_type_specific_negbin,0.0226758046406035,0.0111571406707602,0.0420607456119792,2.44771166883747,1.37121545978538,4.50865449346866,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,5.23811087197941,2.57729949494561,9.71603223636719,47.4318193083395,24.4527583283648,97.2339444096311,2.23811087197941,19.5681806916605,PCV7 +Atlanta.pre.PCV,18C,231,204680,1,0,4,adjusted_type_specific_negbin,0.0032083662597804,0.000794719499692891,0.0108180987789575,2.44771166883747,1.37121545978538,4.50865449346866,0.00271264763861516,0.0014655820441361,0.00510303075337189,3.54405372684984,2.48735345296771,5.1992340148223,0.741132606009272,0.183580204429058,2.49898081793919,4.33987498729322,1.21341015130548,14.6674556357243,0.741132606009272,0.33987498729322,PCV7 +Atlanta.pre.PCV,19A,231,204680,1,8,9,adjusted_type_specific_negbin,0.0300387219531621,0.0143291819050807,0.0554667746731636,2.44771166883747,1.37121545978538,4.50865449346866,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,6.93894477118044,3.31004102007365,12.8128249495008,23.0006215818553,10.1519212359918,52.063307260568,1.06105522881956,14.0006215818553,PCV13 +Atlanta.pre.PCV,19F,231,204680,1,11,30,adjusted_type_specific_negbin,0.0583763898331448,0.0351904088036138,0.0897579609948505,2.44771166883747,1.37121545978538,4.50865449346866,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,13.4849460514564,8.12898443363478,20.7340889898105,18.5783489574006,10.1055552934258,35.1953820097852,2.48494605145645,11.4216510425994,PCV7 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+Atlanta.pre.PCV,6A,231,204680,1,15,15,adjusted_type_specific_negbin,0.068113777480012,0.0423139127281537,0.102601664869021,2.44771166883747,1.37121545978538,4.50865449346866,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,15.7342825978828,9.7745138402035,23.7009845847439,14.6964114516986,7.60149700152973,28.8826496772457,0.734282597882764,0.303588548301448,PCV13 +Atlanta.pre.PCV,6B,231,204680,1,17,24,adjusted_type_specific_negbin,0.0746297979275915,0.0471875464074867,0.111039784606676,2.44771166883747,1.37121545978538,4.50865449346866,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,17.2394833212736,10.9003232201294,25.6501902441421,27.7309837474289,14.4032811842324,55.1973936255744,0.239483321273646,3.73098374742892,PCV7 +Atlanta.pre.PCV,9V,231,204680,1,6,10,adjusted_type_specific_negbin,0.0222500342024037,0.00968190544428711,0.0441621179837114,2.44771166883747,1.37121545978538,4.50865449346866,0.00205287287839593,0.00108874030355059,0.00391932125341218,3.54405372684984,2.48735345296771,5.1992340148223,5.13975790075527,2.23652015763032,10.2014492542373,22.3966310454062,9.1044084865749,57.9061428338564,0.860242099244735,12.3966310454062,PCV7 +Ontario.pre.PCV,11A,1139,580507,1,26,0,adjusted_type_specific_negbin,0.0231348745643176,0.0155453032158046,0.0329702706943047,0.309293655088302,0.164507290814834,0.601537403205112,6.73010459285807e-05,3.04044095768925e-05,0.000137466679604039,3.54405372684984,2.48735345296771,5.1992340148223,26.3506221287578,17.7061003628014,37.5531383208131,0.276598802525951,0.106556897467667,0.690381276543573,0.350622128757777,0.276598802525951,PCV20 +Ontario.pre.PCV,14,1139,580507,1,30,36,adjusted_type_specific_negbin,0.028731507595752,0.0203158972745755,0.0391841116064528,0.309293655088302,0.164507290814834,0.601537403205112,0.00423723681930139,0.00258012255252856,0.00696647306397263,3.54405372684984,2.48735345296771,5.1992340148223,32.7251871515615,23.1398069957415,44.6307031197497,21.7305433102734,11.999694139673,40.7776403943228,2.72518715156153,14.2694566897266,PCV7 +Ontario.pre.PCV,19A,1139,580507,1,16,2,adjusted_type_specific_negbin,0.0139108353016027,0.00838535618937287,0.0215035883906722,0.309293655088302,0.164507290814834,0.601537403205112,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,15.8444414085254,9.5509206996957,24.4925871769756,3.84594673437091,1.83903049645616,8.05377223540208,0.15555859147457,1.84594673437091,PCV13 +Ontario.pre.PCV,19F,1139,580507,1,71,9,adjusted_type_specific_negbin,0.0633671911418205,0.0503587244354357,0.0781252585543731,0.309293655088302,0.164507290814834,0.601537403205112,0.000641946783366467,0.000387370919778733,0.00106697652149807,3.54405372684984,2.48735345296771,5.1992340148223,72.1752307105335,57.3585871319613,88.9846694934309,7.28540465094815,3.87472269459813,14.1101971487177,1.17523071053353,1.71459534905185,PCV7 +Ontario.pre.PCV,23F,1139,580507,1,94,9,adjusted_type_specific_negbin,0.0827573987055193,0.0680488478624485,0.0996317030467467,0.309293655088302,0.164507290814834,0.601537403205112,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,94.2606771255864,77.5076377153288,113.480509770244,10.2370854011141,5.34221328988676,20.0512864827323,0.260677125586426,1.23708540111413,PCV7 +Ontario.pre.PCV,6A,1139,580507,1,67,2,adjusted_type_specific_negbin,0.0584324226021071,0.045937818459956,0.0727190825917406,0.309293655088302,0.164507290814834,0.601537403205112,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,66.5545293438,52.3231752258898,82.8270350719926,4.54366998869858,2.30706566482387,9.04133606228347,0.445470656200001,2.54366998869858,PCV13 +Ontario.pre.PCV,6B,1139,580507,1,108,11,adjusted_type_specific_negbin,0.0950416064348339,0.0791818502562173,0.11270118092551,0.309293655088302,0.164507290814834,0.601537403205112,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,108.252389729276,90.1881274418315,128.366645074156,12.7446608102417,6.8459888793197,24.5703836229943,0.252389729275833,1.74466081024165,PCV7 +Morocco.pre.PCV,19A,200,212566,1,0,10,adjusted_type_specific_negbin,0.00762608894670011,0.00256654534778705,0.0197024646062522,3.23001632264411,1.60436655148718,6.65526510917314,0.00154774085141028,0.00100775736416358,0.00238638210003903,3.54405372684984,2.48735345296771,5.1992340148223,1.52521778934002,0.513309069557409,3.94049292125043,7.99075804639457,3.04401584760732,20.9944749068255,1.52521778934002,2.00924195360543,PCV13 +Morocco.pre.PCV,23A,200,212566,1,5,6,adjusted_type_specific_negbin,0.0338933539796094,0.0163295391564133,0.0620268011769091,3.23001632264411,1.60436655148718,6.65526510917314,0.000158745060861182,8.01460924002509e-05,0.000306977704583806,3.54405372684984,2.48735345296771,5.1992340148223,6.77867079592187,3.26590783128267,12.4053602353818,3.6553095188142,1.502573040704,8.59910246944967,1.77867079592187,2.3446904811858,No PCV +Morocco.pre.PCV,23F,200,212566,1,3,11,adjusted_type_specific_negbin,0.0208445210590261,0.00888599430965526,0.0430541094478312,3.23001632264411,1.60436655148718,6.65526510917314,0.000690112308211118,0.000405240946192111,0.00117048892695758,3.54405372684984,2.48735345296771,5.1992340148223,4.16890421180522,1.77719886193105,8.61082188956623,9.68859581967245,4.15619670787267,22.8152397894938,1.16890421180522,1.31140418032755,PCV7 +Morocco.pre.PCV,3,200,212566,1,0,1,adjusted_type_specific_negbin,0.00133727657988129,0.000152535072712025,0.00689340703333583,3.23001632264411,1.60436655148718,6.65526510917314,0.00203482336000799,0.00122555507102751,0.00343097201199959,3.54405372684984,2.48735345296771,5.1992340148223,0.267455315976257,0.030507014542405,1.37868140666717,1.86250305356242,0.226895141599729,9.28746399254222,0.267455315976257,0.862503053562423,PCV13 +Morocco.pre.PCV,4,200,212566,1,1,0,adjusted_type_specific_negbin,0.00190961460607069,0.000215570737525802,0.00968533594644815,3.23001632264411,1.60436655148718,6.65526510917314,0.00190772142059072,0.000993460219808901,0.0036730064261805,3.54405372684984,2.48735345296771,5.1992340148223,0.381922921214138,0.0431141475051605,1.93706718928963,2.48210690895279,0.295864237374731,13.0698761477787,0.618077078785862,2.48210690895279,PCV7 +Morocco.pre.PCV,6A,200,212566,1,13,34,adjusted_type_specific_negbin,0.0760885404961041,0.0469607048617435,0.115082983955776,3.23001632264411,1.60436655148718,6.65526510917314,0.000432942276798792,0.000258164794710343,0.000727146845603692,3.54405372684984,2.48735345296771,5.1992340148223,15.2177080992208,9.39214097234871,23.0165967911551,22.3793492562687,11.6286054114474,45.4962987316505,2.21770809922081,11.6206507437313,PCV13 +Morocco.pre.PCV,6B,200,212566,1,10,21,adjusted_type_specific_negbin,0.0511092552531762,0.0283320680032878,0.0846562092104389,3.23001632264411,1.60436655148718,6.65526510917314,0.000749081756651293,0.000449556201710222,0.00124361755137026,3.54405372684984,2.48735345296771,5.1992340148223,10.2218510506352,5.66641360065755,16.9312418420878,25.8038736821985,12.1367651591469,58.1578556481666,0.221851050635237,4.80387368219845,PCV7 +Morocco.pre.PCV,8,200,212566,1,1,0,adjusted_type_specific_negbin,0.00189995981125331,0.000210089929743621,0.00998543710794194,3.23001632264411,1.60436655148718,6.65526510917314,0.00191387330730331,0.000891669331639935,0.0040720163095461,3.54405372684984,2.48735345296771,5.1992340148223,0.379991962250662,0.0420179859487242,1.99708742158839,2.44908739247762,0.300737246740801,13.6000500907261,0.620008037749338,2.44908739247762,PCV20 diff --git a/examples/type_specific_strain_modified_strain_invasiveness.png b/examples/type_specific_strain_modified_strain_invasiveness.png new file mode 100644 index 0000000..c4664e7 Binary files /dev/null and b/examples/type_specific_strain_modified_strain_invasiveness.png differ diff --git a/examples/within_serotype_invasiveness_variation_plot.pdf b/examples/within_serotype_invasiveness_variation_plot.pdf new file mode 100644 index 0000000..c81332f Binary files /dev/null and b/examples/within_serotype_invasiveness_variation_plot.pdf differ diff --git a/examples/within_serotype_invasiveness_variation_plot.png b/examples/within_serotype_invasiveness_variation_plot.png new file mode 100644 index 0000000..0a730fd Binary files /dev/null and b/examples/within_serotype_invasiveness_variation_plot.png differ diff --git a/examples/within_strain_invasiveness_variation_plot.pdf b/examples/within_strain_invasiveness_variation_plot.pdf new file mode 100644 index 0000000..806d327 Binary files /dev/null and b/examples/within_strain_invasiveness_variation_plot.pdf differ diff --git a/examples/within_strain_invasiveness_variation_plot.png b/examples/within_strain_invasiveness_variation_plot.png new file mode 100644 index 0000000..239f44c Binary files /dev/null and b/examples/within_strain_invasiveness_variation_plot.png differ diff --git a/inst/stan/adjusted_null_negbin.stan b/inst/stan/adjusted_null_negbin.stan index 7ff4496..5e2de06 100644 --- a/inst/stan/adjusted_null_negbin.stan +++ b/inst/stan/adjusted_null_negbin.stan @@ -27,7 +27,7 @@ parameters { vector[i_max-1] gamma_varying; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -35,7 +35,6 @@ transformed parameters { // declare transformed parameters vector[i_max] gamma_i; - real phi_nb; real mu = 0; // position parameter of Cauchy for gamma real tau = 2; // scale parameter of Cauchy for gamma @@ -49,27 +48,30 @@ transformed parameters { gamma_i[i] = pow(10, mu + tau * tan(gamma_varying[i-1])); } - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability across all types + target += uniform_lpdf(log_nu | -6, 1); + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + // iterate over datasets for (index in 1:n_obs) { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf(log_nu | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/adjusted_null_poisson.stan b/inst/stan/adjusted_null_poisson.stan index 2fd5dd2..0c99022 100644 --- a/inst/stan/adjusted_null_poisson.stan +++ b/inst/stan/adjusted_null_poisson.stan @@ -50,17 +50,21 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability across all types + target += uniform_lpdf(log_nu | -6, 1); + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + // iterate over datasets for (index in 1:n_obs) { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf(log_nu | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); // calculate likelihood given data diff --git a/inst/stan/adjusted_type_specific_negbin.stan b/inst/stan/adjusted_type_specific_negbin.stan index 9f6af56..99162de 100644 --- a/inst/stan/adjusted_type_specific_negbin.stan +++ b/inst/stan/adjusted_type_specific_negbin.stan @@ -27,7 +27,7 @@ parameters { vector[i_max-1] gamma_varying; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -35,7 +35,6 @@ transformed parameters { // declare transformed parameters vector[i_max] gamma_i; - real phi_nb; real mu = 0; // position parameter of Cauchy for gamma real tau = 2; // scale parameter of Cauchy for gamma @@ -51,14 +50,24 @@ transformed parameters { gamma_i[i] = pow(10, mu + tau * tan(gamma_varying[i-1])); } - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + // iterate over datasets for (index in 1:n_obs) { @@ -67,14 +76,9 @@ model { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf( log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/adjusted_type_specific_poisson.stan b/inst/stan/adjusted_type_specific_poisson.stan index b53d063..5c7ab0d 100644 --- a/inst/stan/adjusted_type_specific_poisson.stan +++ b/inst/stan/adjusted_type_specific_poisson.stan @@ -52,6 +52,16 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + // iterate over datasets for (index in 1:n_obs) { @@ -60,12 +70,8 @@ model { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf( log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); // calculate likelihood given data diff --git a/inst/stan/adjusted_type_specific_strain_modified_by_type_negbin.stan b/inst/stan/adjusted_type_specific_strain_modified_by_type_negbin.stan index 60cb6bf..4867532 100644 --- a/inst/stan/adjusted_type_specific_strain_modified_by_type_negbin.stan +++ b/inst/stan/adjusted_type_specific_strain_modified_by_type_negbin.stan @@ -32,7 +32,7 @@ parameters { vector[i_max-1] gamma_varying; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -40,7 +40,6 @@ transformed parameters { // declare transformed parameters vector[i_max] gamma_i; - real phi_nb; real mu = 0; // position parameter of Cauchy for gamma real tau = 2; // scale parameter of Cauchy for gamma real mu_mod = 0; // position parameter of Cauchy for strain invasiveness @@ -64,14 +63,29 @@ transformed parameters { gamma_i[i] = pow(10, mu + tau * tan(gamma_varying[i-1])); } - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -6, 1); + } + + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); + } + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + // iterate over datasets for (index in 1:n_obs) { @@ -83,15 +97,9 @@ model { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf( log_nu_k[k] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); - target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/adjusted_type_specific_strain_modified_by_type_poisson.stan b/inst/stan/adjusted_type_specific_strain_modified_by_type_poisson.stan index b9809d2..0236585 100644 --- a/inst/stan/adjusted_type_specific_strain_modified_by_type_poisson.stan +++ b/inst/stan/adjusted_type_specific_strain_modified_by_type_poisson.stan @@ -65,6 +65,21 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); + } + + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -6, 1); + } + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + // iterate over datasets for (index in 1:n_obs) { @@ -76,14 +91,9 @@ model { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf( log_nu_k[k] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/adjusted_type_specific_type_modified_by_strain_negbin.stan b/inst/stan/adjusted_type_specific_type_modified_by_strain_negbin.stan index a8330d3..2808d12 100644 --- a/inst/stan/adjusted_type_specific_type_modified_by_strain_negbin.stan +++ b/inst/stan/adjusted_type_specific_type_modified_by_strain_negbin.stan @@ -32,7 +32,7 @@ parameters { vector[i_max-1] gamma_varying; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -40,7 +40,6 @@ transformed parameters { // declare transformed parameters vector[i_max] gamma_i; - real phi_nb; real mu = 0; // position parameter of Cauchy for gamma real tau = 2; // scale parameter of Cauchy for gamma real mu_mod = 0; // position parameter of Cauchy for strain invasiveness @@ -64,14 +63,29 @@ transformed parameters { gamma_i[i] = pow(10, mu + tau * tan(gamma_varying[i-1])); } - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); + } + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + // iterate over datasets for (index in 1:n_obs) { @@ -83,15 +97,9 @@ model { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf( log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); - target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/adjusted_type_specific_type_modified_by_strain_poisson.stan b/inst/stan/adjusted_type_specific_type_modified_by_strain_poisson.stan index 38d6ea2..72c6f61 100644 --- a/inst/stan/adjusted_type_specific_type_modified_by_strain_poisson.stan +++ b/inst/stan/adjusted_type_specific_type_modified_by_strain_poisson.stan @@ -65,6 +65,21 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); + } + + // Calculate prior probability for study adjustment + for (i in 2:i_max) { + target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); + } + // iterate over datasets for (index in 1:n_obs) { @@ -76,14 +91,9 @@ model { // Get location adjustment int i = i_values[index]; - if (i > 1) { - target += uniform_lpdf(gamma_varying[i-1] | -pi()/2, pi()/2); - } - // calculate prior probability - target += uniform_lpdf( log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/null_negbin.stan b/inst/stan/null_negbin.stan index 6ab12ce..969f049 100644 --- a/inst/stan/null_negbin.stan +++ b/inst/stan/null_negbin.stan @@ -24,7 +24,7 @@ parameters { real log_nu; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -32,30 +32,30 @@ parameters { transformed parameters { real nu; - real phi_nb; // calculate invasiveness on a real scale // vector[j_max] nu_j; nu = pow(10,log_nu); - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability across all types + target += uniform_lpdf(log_nu | -6, 1); + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + // iterate over datasets for (index in 1:n_obs) { // Get serotype int j = j_values[index]; - // calculate prior probability - target += uniform_lpdf( log_nu | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/null_poisson.stan b/inst/stan/null_poisson.stan index d6d8334..9293be1 100644 --- a/inst/stan/null_poisson.stan +++ b/inst/stan/null_poisson.stan @@ -38,14 +38,16 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability across all types + target += uniform_lpdf(log_nu | -6, 1); + // iterate over datasets for (index in 1:n_obs) { // Get serotype int j = j_values[index]; - // calculate prior probability - target += uniform_lpdf( log_nu | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); // calculate likelihood given data diff --git a/inst/stan/type_specific_negbin.stan b/inst/stan/type_specific_negbin.stan index 0315fa4..36a2108 100644 --- a/inst/stan/type_specific_negbin.stan +++ b/inst/stan/type_specific_negbin.stan @@ -24,7 +24,7 @@ parameters { vector[j_max] log_nu_j; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -32,30 +32,32 @@ transformed parameters { // calculate invasiveness on a real scale vector[j_max] nu_j; - real phi_nb; for (j in 1:j_max) { nu_j[j] = pow(10, log_nu_j[j]); } - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + // iterate over datasets for (index in 1:n_obs) { // Get serotype int j = j_values[index]; - // calculate prior probability - target += uniform_lpdf( log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/type_specific_poisson.stan b/inst/stan/type_specific_poisson.stan index 6aed7ce..7c6d04f 100644 --- a/inst/stan/type_specific_poisson.stan +++ b/inst/stan/type_specific_poisson.stan @@ -38,14 +38,18 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + // iterate over datasets for (index in 1:n_obs) { // Get serotype int j = j_values[index]; - // calculate prior probability - target += uniform_lpdf( log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); // calculate likelihood given data diff --git a/inst/stan/type_specific_strain_modified_by_type_negbin.stan b/inst/stan/type_specific_strain_modified_by_type_negbin.stan index 80a177d..d220793 100644 --- a/inst/stan/type_specific_strain_modified_by_type_negbin.stan +++ b/inst/stan/type_specific_strain_modified_by_type_negbin.stan @@ -29,7 +29,7 @@ parameters { vector[j_max] log_nu_j; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -38,7 +38,6 @@ transformed parameters { // declare transformed parameters vector[k_max] nu_k; vector[j_max] nu_j; - real phi_nb; real mu_mod = 0; // position parameter of Cauchy for strain invasiveness real tau_mod = 0.5; // scale parameter of Cauchy for strain invasiveness @@ -52,14 +51,24 @@ transformed parameters { nu_k[k] = pow(10, log_nu_k[k]); } - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); + } + + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -6, 1); + } + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + // iterate over datasets for (index in 1:n_obs) { @@ -72,12 +81,8 @@ model { // Get location adjustment int i = i_values[index]; - // calculate prior probability - target += uniform_lpdf( log_nu_k[k] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); - //target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); - target += uniform_lpdf(log_nu_j[j] | -10, 10); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/type_specific_strain_modified_by_type_poisson.stan b/inst/stan/type_specific_strain_modified_by_type_poisson.stan index 3d002c6..aac1f2e 100644 --- a/inst/stan/type_specific_strain_modified_by_type_poisson.stan +++ b/inst/stan/type_specific_strain_modified_by_type_poisson.stan @@ -53,6 +53,16 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); + } + + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -6, 1); + } + // iterate over datasets for (index in 1:n_obs) { @@ -65,10 +75,8 @@ model { // Get location adjustment int i = i_values[index]; - // calculate prior probability - target += uniform_lpdf(log_nu_k[k] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_nu_j[j] | -1.25, 1.25); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/type_specific_type_modified_by_strain_negbin.stan b/inst/stan/type_specific_type_modified_by_strain_negbin.stan index 90cd0dd..374aa43 100644 --- a/inst/stan/type_specific_type_modified_by_strain_negbin.stan +++ b/inst/stan/type_specific_type_modified_by_strain_negbin.stan @@ -29,7 +29,7 @@ parameters { vector[k_max-1-1] log_nu_k; // negative binomial overdispersions - real log_phi_nb; + real phi_nb; } @@ -38,7 +38,6 @@ transformed parameters { // declare transformed parameters vector[j_max] nu_j; vector[k_max] nu_k; - real phi_nb; real mu_mod = 0; // position parameter of Cauchy for strain invasiveness real tau_mod = 1; // scale parameter of Cauchy for strain invasiveness @@ -53,14 +52,24 @@ transformed parameters { nu_k[k] = pow(10, log_nu_k[k-1]); } - // calculate negative binomial overdispersion - phi_nb = pow(10, log_phi_nb); - } // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); + } + + // Calculate prior probability for precision parameter + target += exponential_lpdf(phi_nb | 1); + // iterate over datasets for (index in 1:n_obs) { @@ -73,11 +82,8 @@ model { // Get location adjustment int i = i_values[index]; - // calculate prior probability - target += uniform_lpdf( log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_phi_nb | -3, 3); - target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]); diff --git a/inst/stan/type_specific_type_modified_by_strain_poisson.stan b/inst/stan/type_specific_type_modified_by_strain_poisson.stan index af21140..b7d4f24 100644 --- a/inst/stan/type_specific_type_modified_by_strain_poisson.stan +++ b/inst/stan/type_specific_type_modified_by_strain_poisson.stan @@ -53,6 +53,16 @@ transformed parameters { // The model to be estimated model { + // Calculate prior probability for types + for (j in 1:j_max) { + target += uniform_lpdf(log_nu_j[j] | -6, 1); + } + + // Calculate prior probability for strains + for (k in 1:k_max) { + target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); + } + // iterate over datasets for (index in 1:n_obs) { @@ -65,10 +75,8 @@ model { // Get location adjustment int i = i_values[index]; - // calculate prior probability - target += uniform_lpdf(log_nu_j[j] | -6, 1); + // Calculate prior probability for carriage frequency target += beta_lpdf(rho_ij[index] | 1, 1); - target += uniform_lpdf(log_nu_k[k] | -1.25, 1.25); // calculate likelihood given data target += binomial_lpmf(c_ij[index] | n_i[index], rho_ij[index]);