Merge 295eebe into d7f66d7

epiverse-trace · Aug 3, 2023 · ba1740a · ba1740a
2 parents d7f66d7 + 295eebe
commit ba1740a
Show file tree

Hide file tree

Showing 3 changed files with 18 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,7 +38,8 @@ LazyData: true
 RoxygenNote: 7.2.3
 Depends: 
     R (>= 3.5.0)
-Imports: 
+Imports:
+    checkmate,
     methods,
     Rcpp (>= 0.12.0),
     RcppParallel (>= 5.0.1),

diff --git a/R/modelling.R b/R/modelling.R
@@ -49,13 +49,15 @@
 #' }
 #' @export
 run_seromodel <- function(serodata,
-                          foi_model = "constant",
+                          foi_model = c("constant", "tv_normal_log",
+                                        "tv_normal"),
                           n_iters = 1000,
                           n_thin = 2,
                           delta = 0.90,
                           m_treed = 10,
                           decades = 0,
                           print_summary = TRUE) {
+  foi_model <- match.arg(foi_model)
   survey <- unique(serodata$survey)
   if (length(survey) > 1) warning("You have more than 1 surveys or survey codes")
   seromodel_object <- fit_seromodel(serodata = serodata,
@@ -122,13 +124,15 @@ run_seromodel <- function(serodata,
 #'
 #' @export
 fit_seromodel <- function(serodata,
-                          foi_model,
+                          foi_model = c("constant", "tv_normal_log",
+                                        "tv_normal"),
                           n_iters = 1000,
                           n_thin = 2,
                           delta = 0.90,
                           m_treed = 10,
                           decades = 0) {
   # TODO Add a warning because there are exceptions where a minimal amount of iterations is needed
+  foi_model <- match.arg(foi_model)
   model <- stanmodels[[foi_model]]
   exposure_ages <- get_exposure_ages(serodata)
   exposure_years <- (min(serodata$birth_year):serodata$tsur[1])[-1]

diff --git a/R/seroprevalence_data.R b/R/seroprevalence_data.R
@@ -37,6 +37,16 @@
 prepare_serodata <- function(serodata = serodata,
                             alpha = 0.05, 
                             add_age_mean_f = TRUE) {
+  checkmate::assert_numeric(alpha, lower = 0, upper = 1)
+  checkmate::assert_logical(add_age_mean_f)
+  #Check that serodata has the right columns
+  stopifnot("serodata must contain the right columns" =
+            setequal(names(serodata),
+                     c("survey", "total", "counts", "age_min","age_max",
+                       "tsur", "country","test", "antibody"
+                       )
+                     )
+            )
   if(add_age_mean_f){
     serodata <- serodata %>%
       dplyr::mutate(age_mean_f = floor((age_min + age_max) / 2), sample_size = sum(total)) %>%