Simulation functions and vignette plus other things

DESCRIPTION

@@ -52,7 +52,10 @@ Imports:
     ggplot2,
     Hmisc,
     loo,
-    purrr
+    purrr,
+    tidyr,
+    tibble,
+    Matrix
 LinkingTo: 
     BH (>= 1.66.0),
     Rcpp (>= 0.12.0),

NAMESPACE

@@ -2,23 +2,26 @@
 
 export(extract_seromodel_summary)
 export(fit_seromodel)
-export(generate_sim_data)
 export(get_chunk_structure)
 export(get_cohort_ages)
 export(get_foi_central_estimates)
 export(get_prev_expanded)
-export(get_sim_n_seropositive)
-export(get_sim_probability)
 export(get_table_rhats)
-export(group_sim_data)
 export(plot_foi)
 export(plot_info_table)
 export(plot_rhats)
 export(plot_seromodel)
 export(plot_seroprev)
 export(plot_seroprev_fitted)
 export(prepare_serodata)
+export(probability_seropositive_by_age)
+export(probability_seropositive_general_model_by_age)
 export(run_seromodel)
+export(simulate_serosurvey)
+export(simulate_serosurvey_age_and_time_model)
+export(simulate_serosurvey_age_model)
+export(simulate_serosurvey_general_model)
+export(simulate_serosurvey_time_model)
 import(Rcpp)
 import(dplyr)
 import(methods)

R/modelling.R

@@ -468,12 +468,13 @@ get_chunk_structure <- function(
 #' cohort_ages <- get_cohort_ages(serodata = serodata)
 #' @export
 get_cohort_ages <- function(serodata) {
-  birth_year <- (min(serodata$birth_year):serodata$tsur[1])
-  age <- (seq_along(min(serodata$birth_year):(serodata$tsur[1] - 1)))
+
+  birth_year <- min(serodata$birth_year):(serodata$tsur[1] - 1)
+  age <- rev(seq_along(birth_year))
 
   cohort_ages <- data.frame(
-    birth_year = birth_year[-length(birth_year)],
-    age = rev(age)
+    birth_year = birth_year,
+    age = age
   )
   return(cohort_ages)
 }
@@ -507,9 +508,8 @@ get_exposure_matrix <- function(serodata) {
 #' Extract central estimates for the fitted forced FoI
 #'
 #' @param seromodel_object Stanfit object containing the results of fitting a
-#'   model by means of [run_seromodel].
-#' @param cohort_ages  A data frame containing the age of each cohort
-#'   corresponding to each birth year.
+#'   model by means of [fit_seromodel].
+#' @inheritParams fit_seromodel
 #' @param lower_quantile Lower quantile used to compute the credible interval of
 #' the fitted force-of-infection.
 #' @param upper_quantile Lower quantile used to compute the credible interval of
@@ -525,18 +525,18 @@ get_exposure_matrix <- function(serodata) {
 #' cohort_ages <- get_cohort_ages(serodata = serodata)
 #' foi_central_estimates <- get_foi_central_estimates(
 #'   seromodel_object = seromodel_object,
-#'   cohort_ages = cohort_ages
+#'   serodata = serodata
 #' )
 #' @export
 get_foi_central_estimates <- function(
     seromodel_object,
-    cohort_ages,
+    serodata,
     lower_quantile = 0.05,
     upper_quantile = 0.95
     ) {
   # extracts force-of-infection from stan fit
   foi <- rstan::extract(seromodel_object, "foi", inc_warmup = FALSE)[[1]]
-
+  cohort_ages <- get_cohort_ages(serodata)
   # defines time scale depending on the type of the model
   if(
     seromodel_object@model_name %in%