Add input validation (#92)

* Added argument matching in fit_seromodel()

* Added allowed options to arg foi_model

* Added input validation to prepare_serodata()

* Fixed the check for required columns

* Regenerated the docs

---------

Co-authored-by: ntorresd <[email protected]>

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),

R/modelling.R

@@ -48,13 +48,15 @@
 #'                foi_model = "constant")
 #' @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,
@@ -102,13 +104,15 @@ 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]]
   cohort_ages <- get_cohort_ages(serodata = serodata)
   exposure_matrix <- get_exposure_matrix(serodata)

R/seroprevalence_data.R

@@ -33,14 +33,25 @@
 #' @export
 prepare_serodata <- function(serodata = serodata,
                             alpha = 0.05) {
+  checkmate::assert_numeric(alpha, lower = 0, upper = 1)
+  #Check that serodata has the right columns
+  stopifnot("serodata must contain the right columns" =
+            all(c("survey", "total", "counts", "age_min", "age_max", "tsur",
+                  "country","test","antibody"
+                  ) %in%
+                  colnames(serodata)
+                )
+            )
   if(!any(colnames(serodata) == "age_mean_f")){
     serodata <- serodata %>%
       dplyr::mutate(age_mean_f = floor((age_min + age_max) / 2), sample_size = sum(total))
   }  
+
   if(!any(colnames(serodata) == "birth_year")){
     serodata <- serodata %>%
       dplyr::mutate(birth_year = .data$tsur - .data$age_mean_f)
   }
+
   serodata <- serodata %>%
     cbind(
       Hmisc::binconf(