Merge dev into main

.github/workflows/R-CMD-check.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 

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),
@@ -57,7 +58,6 @@ Imports:
     purrr,
     qtl,
     reshape2,
-    tidyverse,
     usethis,
     vdiffr (>= 1.0.0)    
 LinkingTo: 

NAMESPACE

@@ -2,8 +2,9 @@
 
 export(extract_seromodel_summary)
 export(fit_seromodel)
-export(get_exposure_ages)
+export(get_cohort_ages)
 export(get_exposure_matrix)
+export(get_foi_central_estimates)
 export(get_prev_expanded)
 export(get_table_rhats)
 export(plot_foi)

R/model_comparison.R

@@ -1,26 +1,27 @@
 #' Method for extracting a dataframe containing the R-hat estimates for a given serological model
 #' 
 #' This method relies in the function \link[bayesplot]{rhat} to extract the R-hat estimates of the serological model object 
-#' \code{seromodel_object} and returns a table a dataframe with the estimates for each year of birth. 
-#' @param seromodel_object seromodel_object
+#' \code{seromodel_object} and returns a table a dataframe with the estimates for each year of birth.
+#' @inheritParams get_foi_central_estimates
 #' @return rhats table
 #' @examples
-#' \dontrun{
-#' data("serodata")
-#' data_test <- prepare_serodata(serodata = serodata)
-#' model_constant <- run_seromodel(serodata = data_test, 
-#'                                 foi_model = "constant", 
+#' data(chagas2012)
+#' serodata <- prepare_serodata(serodata = chagas2012)
+#' model_constant <- run_seromodel(serodata = serodata,
+#'                                 foi_model = "constant",
 #'                                 n_iters = 1500)
-#' get_table_rhats(model_object = model_constant)
-#' }
+#' cohort_ages <- get_cohort_ages(serodata)
+#' get_table_rhats(seromodel_object = model_constant,
+#'                 cohort_ages = cohort_ages)
 #' @export
-get_table_rhats <- function(seromodel_object) {
-  rhats <- bayesplot::rhat(seromodel_object$fit, "foi")
+get_table_rhats <- function(seromodel_object,
+                            cohort_ages) {
+  rhats <- bayesplot::rhat(seromodel_object, "foi")
 
   if (any(is.nan(rhats))) {
     rhats[which(is.nan(rhats))] <- 0
   }
-  model_rhats <- data.frame(year = seromodel_object$exposure_years, rhat = rhats)
+  model_rhats <- data.frame(year = cohort_ages$birth_year, rhat = rhats)
   model_rhats$rhat[model_rhats$rhat == 0] <- NA
 
   return(model_rhats)