Fixed issues in exposure timings

seroanalytics · Oct 24, 2024 · 34094e1 · 34094e1
1 parent 03579f7
commit 34094e1
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Showing 58 changed files with 88 additions and 480 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
 outputs/fits/*
-
+vignettes/int/*
 # Except for the simulate_data directory
 !outputs/fits/simulated_data/
 

diff --git a/R/.DS_Store b/R/.DS_Store
diff --git a/R/postprocess.R b/R/postprocess.R
@@ -283,6 +283,7 @@ plot_inf_rec <- function(model_summary, file_path) {
     ggsave(here::here(file_path, "infection_recov.png"), height = 10, width = 10)
 }
 
+
 plot_cop_rec <- function(model_summary, file_path) {
 
     fitfull <- model_summary$fit    

diff --git a/R/utils_model.R b/R/utils_model.R
@@ -243,8 +243,10 @@ createSeroJumpModel <- function(
         sample(1:length(exp_prior_list[[i]]), 1, prob = exp_prior_list[[i]]) 
     }
 
-    check_exposures_times(data_sero, data_known, exposureTypes, exposureFitted, exposurePriorTime, exposurePriorTimeType)
-
+    if (!is.null(data_known)) {
+        check_exposures_times(data_sero, data_known, exposureTypes, exposureFitted, exposurePriorTime, exposurePriorTimeType)
+    }
+
     data_t$exp_list <- exp_prior_list
     data_t$exp_prior <- exp_prior
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/cs1_sim_recovery.html b/docs/articles/cs1_sim_recovery.html
diff --git a/docs/articles/cs2_sarscov2.html → docs/articles/cs2_sarscov2 copy.html b/docs/articles/cs2_sarscov2.html → docs/articles/cs2_sarscov2 copy.html
diff --git a/...2_files/figure-html/unnamed-chunk-5-1.png → ...y_files/figure-html/unnamed-chunk-5-1.png b/...2_files/figure-html/unnamed-chunk-5-1.png → ...y_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/cs2_sarscov2 copy_files/figure-html/unnamed-chunk-5-2.png b/docs/articles/cs2_sarscov2 copy_files/figure-html/unnamed-chunk-5-2.png
diff --git a/...2_files/figure-html/unnamed-chunk-8-1.png → ...y_files/figure-html/unnamed-chunk-7-1.png b/...2_files/figure-html/unnamed-chunk-8-1.png → ...y_files/figure-html/unnamed-chunk-7-1.png
diff --git a/docs/articles/cs2_sarscov2 copy_files/figure-html/unnamed-chunk-7-2.png b/docs/articles/cs2_sarscov2 copy_files/figure-html/unnamed-chunk-7-2.png
diff --git a/docs/articles/cs2_sarscov2_files/figure-html/unnamed-chunk-5-2.png b/docs/articles/cs2_sarscov2_files/figure-html/unnamed-chunk-5-2.png
diff --git a/docs/articles/cs2_sarscov2_files/figure-html/unnamed-chunk-8-2.png b/docs/articles/cs2_sarscov2_files/figure-html/unnamed-chunk-8-2.png
diff --git a/docs/articles/data_format.html b/docs/articles/data_format.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/model_define.html b/docs/articles/model_define.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -283,6 +283,7 @@ plot_inf_rec <- function(model_summary, file_path) { @@
         ggsave(here::here(file_path, "infection_recov.png"), height = 10, width = 10)
     }
     plot_cop_rec <- function(model_summary, file_path) {
         fitfull <- model_summary$fit
@@ Expand Down @@