res <- mod$simulate_population_trajectories()
+#> INFO [2024-10-23 12:39:32] Summarising fits
+#> INFO [2024-10-23 12:39:35] Adjusting by regression coefficients
+#> INFO [2024-10-23 12:39:38] Summarising into quantiles
head(res)
#> time_since_last_exp me lo hi titre_type infection_history
#> <int> <num> <num> <num> <char> <char>
@@ -188,6 +191,11 @@ Figure 4
res <- mod$population_stationary_points(n_draws = 2000)
+#> INFO [2024-10-23 12:39:39] Extracting parameters
+#> INFO [2024-10-23 12:39:39] Adjusting by covariates
+#> INFO [2024-10-23 12:39:39] Calculating peak and switch titre values
+#> INFO [2024-10-23 12:39:39] Recovering covariate names
+#> INFO [2024-10-23 12:39:39] Calculating medians
head(res)
#> infection_history titre_type mu_p mu_s rel_drop_me mu_p_me mu_s_me
#> <char> <char> <num> <num> <num> <num> <num>
@@ -253,9 +261,15 @@ Figure 5
res <- mod$simulate_individual_trajectories(n_draws = 250)
+#> INFO [2024-10-23 12:39:40] Extracting parameters
+#> INFO [2024-10-23 12:39:44] Simulating individual trajectories
+#> INFO [2024-10-23 12:39:48] Recovering covariate names
+#> INFO [2024-10-23 12:39:49] Calculating exposure days. Adjusting exposures by 0 days
+#> INFO [2024-10-23 12:39:52] Resampling
#> Registered S3 method overwritten by 'mosaic':
#> method from
#> fortify.SpatialPolygonsDataFrame ggplot2
+#> INFO [2024-10-23 12:40:02] Summarising into population quantiles
head(res)
#> calendar_day titre_type me lo hi time_shift
#> <IDat> <char> <num> <num> <num> <num>
@@ -334,6 +348,72 @@ Figure 5 shift <- time_shift_values[index]
mod$simulate_individual_trajectories(n_draws = 50, time_shift = shift)
})
+#> INFO [2024-10-23 12:40:03] Extracting parameters
+#> INFO [2024-10-23 12:40:06] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:07] Recovering covariate names
+#> INFO [2024-10-23 12:40:07] Calculating exposure days. Adjusting exposures by -75 days
+#> INFO [2024-10-23 12:40:08] Resampling
+#> INFO [2024-10-23 12:40:10] Summarising into population quantiles
+#> INFO [2024-10-23 12:40:10] Extracting parameters
+#> INFO [2024-10-23 12:40:14] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:14] Recovering covariate names
+#> INFO [2024-10-23 12:40:14] Calculating exposure days. Adjusting exposures by -60 days
+#> INFO [2024-10-23 12:40:15] Resampling
+#> INFO [2024-10-23 12:40:17] Summarising into population quantiles
+#> INFO [2024-10-23 12:40:17] Extracting parameters
+#> INFO [2024-10-23 12:40:21] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:21] Recovering covariate names
+#> INFO [2024-10-23 12:40:21] Calculating exposure days. Adjusting exposures by -45 days
+#> INFO [2024-10-23 12:40:22] Resampling
+#> INFO [2024-10-23 12:40:23] Summarising into population quantiles
+#> INFO [2024-10-23 12:40:24] Extracting parameters
+#> INFO [2024-10-23 12:40:27] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:28] Recovering covariate names
+#> INFO [2024-10-23 12:40:28] Calculating exposure days. Adjusting exposures by -30 days
+#> INFO [2024-10-23 12:40:28] Resampling
+#> INFO [2024-10-23 12:40:30] Summarising into population quantiles
+#> INFO [2024-10-23 12:40:31] Extracting parameters
+#> INFO [2024-10-23 12:40:34] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:35] Recovering covariate names
+#> INFO [2024-10-23 12:40:35] Calculating exposure days. Adjusting exposures by -15 days
+#> INFO [2024-10-23 12:40:35] Resampling
+#> INFO [2024-10-23 12:40:37] Summarising into population quantiles
+#> INFO [2024-10-23 12:40:38] Extracting parameters
+#> INFO [2024-10-23 12:40:41] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:42] Recovering covariate names
+#> INFO [2024-10-23 12:40:42] Calculating exposure days. Adjusting exposures by 0 days
+#> INFO [2024-10-23 12:40:43] Resampling
+#> INFO [2024-10-23 12:40:45] Summarising into population quantiles
+#> INFO [2024-10-23 12:40:45] Extracting parameters
+#> INFO [2024-10-23 12:40:49] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:49] Recovering covariate names
+#> INFO [2024-10-23 12:40:49] Calculating exposure days. Adjusting exposures by 15 days
+#> INFO [2024-10-23 12:40:50] Resampling
+#> INFO [2024-10-23 12:40:52] Summarising into population quantiles
+#> INFO [2024-10-23 12:40:53] Extracting parameters
+#> INFO [2024-10-23 12:40:56] Simulating individual trajectories
+#> INFO [2024-10-23 12:40:57] Recovering covariate names
+#> INFO [2024-10-23 12:40:57] Calculating exposure days. Adjusting exposures by 30 days
+#> INFO [2024-10-23 12:40:57] Resampling
+#> INFO [2024-10-23 12:40:59] Summarising into population quantiles
+#> INFO [2024-10-23 12:41:00] Extracting parameters
+#> INFO [2024-10-23 12:41:03] Simulating individual trajectories
+#> INFO [2024-10-23 12:41:04] Recovering covariate names
+#> INFO [2024-10-23 12:41:04] Calculating exposure days. Adjusting exposures by 45 days
+#> INFO [2024-10-23 12:41:04] Resampling
+#> INFO [2024-10-23 12:41:06] Summarising into population quantiles
+#> INFO [2024-10-23 12:41:07] Extracting parameters
+#> INFO [2024-10-23 12:41:10] Simulating individual trajectories
+#> INFO [2024-10-23 12:41:11] Recovering covariate names
+#> INFO [2024-10-23 12:41:11] Calculating exposure days. Adjusting exposures by 60 days
+#> INFO [2024-10-23 12:41:11] Resampling
+#> INFO [2024-10-23 12:41:13] Summarising into population quantiles
+#> INFO [2024-10-23 12:41:14] Extracting parameters
+#> INFO [2024-10-23 12:41:17] Simulating individual trajectories
+#> INFO [2024-10-23 12:41:18] Recovering covariate names
+#> INFO [2024-10-23 12:41:18] Calculating exposure days. Adjusting exposures by 75 days
+#> INFO [2024-10-23 12:41:18] Resampling
+#> INFO [2024-10-23 12:41:20] Summarising into population quantiles
combined_data <- data.table::data.table(data.table::rbindlist(results_list))
Plotting the median values:
diff --git a/pkgdown.yml b/pkgdown.yml
index 5c27a78..d6d689b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,4 +5,4 @@ articles:
biokinetics: biokinetics.html
data: data.html
model: model.html
-last_built: 2024-10-17T16:14Z
+last_built: 2024-10-23T12:35Z