Fixes #115 (#116)

R/model_comparison.R

@@ -5,14 +5,12 @@
 #' @param seromodel_object seromodel_object
 #' @return rhats table
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' data_test <- prepare_serodata(serodata = chagas2012)
 #' model_constant <- run_seromodel(serodata = data_test,
 #'                                 foi_model = "constant",
 #'                                 n_iters = 1500)
-#' get_table_rhats(model_object = model_constant)
-#' }
+#' get_table_rhats(seromodel_object = model_constant)
 #' @export
 get_table_rhats <- function(seromodel_object) {
   rhats <- bayesplot::rhat(seromodel_object$seromodel_fit, "foi")

R/modelling.R

@@ -42,11 +42,10 @@
 #' @param print_summary TBD
 #' @return \code{seromodel_object}. An object containing relevant information about the implementation of the model. For further details refer to \link{fit_seromodel}.
 #' @examples
-#' \dontrun{
+#' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' run_seromodel (chagas2012,
+#' run_seromodel (serodata,
 #'                foi_model = "constant")
-#' }
 #' @export
 run_seromodel <- function(serodata,
                           foi_model = "constant",
@@ -114,12 +113,10 @@ run_seromodel <- function(serodata,
 #' }
 
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' seromodel_fit <- fit_seromodel(serodata = serodata,
 #'                                foi_model = "constant")
-#' }
 #'
 #' @export
 fit_seromodel <- function(serodata,
@@ -203,11 +200,9 @@ fit_seromodel <- function(serodata,
 #' @param serodata A data frame containing the data from a seroprevalence survey. This data frame must contain the year of birth for each individual (birth_year) and the time of the survey (tsur). birth_year can be constructed by means of the \link{prepare_serodata} function.
 #' @return \code{exposure_ages}. An atomic vector with the numeration of the exposition years in serodata
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(serodata = chagas2012, alpha = 0.05)
 #' exposure_ages <- get_exposure_ages(serodata)
-#' }
 #' @export
 get_exposure_ages <- function(serodata) {
   return(seq_along(min(serodata$birth_year):(serodata$tsur[1] - 1)))
@@ -219,11 +214,9 @@ get_exposure_ages <- function(serodata) {
 #' @param serodata A data frame containing the data from a seroprevalence survey. This data frame must contain the year of birth for each individual (birth_year) and the time of the survey (tsur). birth_year can be constructed by means of the \link{prepare_serodata} function.
 #' @return \code{exposure_output}. An atomic matrix containing the expositions for each entry of \code{serodata} by year.
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(serodata = chagas2012)
 #' exposure_matrix <- get_exposure_matrix(serodata = serodata)
-#' }
 #' @export
 get_exposure_matrix <- function(serodata) {
   age_class <- serodata$age_mean_f
@@ -242,14 +235,11 @@ get_exposure_matrix <- function(serodata) {
 #' generated by means of \link{get_exposure_ages}.
 #' @return \code{foi_central_estimates}. Central estimates for the fitted forced FoI
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- fit_seromodel(serodata = serodata,
 #'                                   foi_model = "constant")
 #' foi_central_estimates <- get_foi_central_estimates(seromodel_object)
-#' }
-#'
 #' @export
 get_foi_central_estimates <- function(seromodel_object) {
 
@@ -301,13 +291,11 @@ get_foi_central_estimates <- function(seromodel_object) {
 #' \code{converged} \tab convergence \cr \tab \cr
 #' }
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(serodata = serodata,
 #'                                   foi_model = "constant")
 #' extract_seromodel_summary(seromodel_object)
-#' }
 #' @export
 extract_seromodel_summary <- function(seromodel_object) {
   #------- Loo estimates
@@ -352,14 +340,12 @@ extract_seromodel_summary <- function(seromodel_object) {
 #' @param bin_data TBD
 #' @return \code{prev_final}. The expanded prevalence data. This is used for plotting purposes in the \code{visualization} module.
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(serodata = serodata,
 #'                           foi_model = "constant")
 #' foi <- rstan::extract(seromodel_object$seromodel_fit, "foi")[[1]]
-#' get_prev_expanded <- function(foi, serodata)
-#' }
+#' get_prev_expanded(foi, serodata)
 #' @export
 get_prev_expanded <- function(foi,
                               serodata,

R/seroprevalence_data.R

@@ -29,10 +29,8 @@
 #' \code{prev_obs_upper} \tab Upper limit of the confidence interval for the observed prevalence \cr \tab \cr
 #' }
 #' @examples
-#'\dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' }
 #' @export
 prepare_serodata <- function(serodata = serodata,
                             alpha = 0.05, 
@@ -90,10 +88,9 @@ prepare_serodata <- function(serodata = serodata,
 #' The last six colums can be added to \code{serodata} by means of the function \code{\link{prepare_serodata}}.
 #' @return data set with the binomial confidence intervals
 #' @examples
-#'\dontrun{
 #' data(chagas2012)
-#' prepare_bin_data(chagas2012)
-#' }
+#' serodata <- prepare_serodata(chagas2012)
+#' prepare_bin_data(serodata)
 #' @export
 prepare_bin_data <- function(serodata) {
   serodata$cut_ages <-

R/visualisation.R

@@ -16,16 +16,9 @@
 #' @param size_text Text size use in the theme of the graph returned by the function.
 #' @return A ggplot object containing the seropositivity-vs-age graph of the raw data of a given seroprevalence survey with its corresponging binomial confidence interval.
 #' @examples
-#' \dontrun{
-#'  data(chagas2012)
-#'  serodata <- prepare_serodata(chagas2012)
-#'  seromodel_object <- run_seromodel(
-#'  serodata = serodata,
-#'  foi_model = "constant",
-#'  n_iters = 1000
-#')
-#' plot_seroprev(seromodel_object, size_text = 15)
-#' }
+#' data(chagas2012)
+#' serodata <- prepare_serodata(chagas2012)
+#' plot_seroprev(serodata, size_text = 15)
 #' @export
 plot_seroprev <- function(serodata,
                           size_text = 6) {
@@ -52,14 +45,12 @@ plot_seroprev <- function(serodata,
 #' @param size_text Text size of the graph returned by the function.
 #' @return A ggplot object containing the seropositivity-vs-age graph including the data, the fitted model and their corresponding confindence intervals.
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(serodata = serodata,
 #'                                   foi_model = "constant",
 #'                                   n_iters = 1000)
 #' plot_seroprev_fitted(seromodel_object, size_text = 15)
-#' }
 #' @export
 plot_seroprev_fitted <- function(seromodel_object,
                                  size_text = 6) {
@@ -133,7 +124,6 @@ plot_seroprev_fitted <- function(seromodel_object,
 #' @param foi_sim TBD
 #' @return A ggplot2 object containing the Force-of-infection-vs-time including the corresponding confidence interval.
 #' @examples
-#' \dontrun{
 #'  data(chagas2012)
 #'  serodata <- prepare_serodata(chagas2012)
 #'  seromodel_object <- run_seromodel(
@@ -142,7 +132,6 @@ plot_seroprev_fitted <- function(seromodel_object,
 #'    n_iters = 1000
 #'  )
 #' plot_foi(seromodel_object, size_text = 15)
-#' }
 #' @export
 plot_foi <- function(seromodel_object,
                      max_lambda = NA,
@@ -229,7 +218,6 @@ plot_foi <- function(seromodel_object,
 #' @param size_text Text size use in the theme of the graph returned by the function.
 #' @return The rhats-convergence plot of the selected model.
 #' @examples
-#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(
@@ -239,7 +227,6 @@ plot_foi <- function(seromodel_object,
 #'  )
 #' plot_rhats(seromodel_object,
 #'            size_text = 15)
-#' }
 #' @export
 plot_rhats <- function(seromodel_object,
                        size_text = 25) {
@@ -295,7 +282,6 @@ plot_rhats <- function(seromodel_object,
 #' @param foi_sim TBD
 #' @return A ggplot object with a vertical arrange containing the seropositivity, force of infection, and convergence plots.
 #' @examples
-#' \dontrun{
 #'  data(chagas2012)
 #'  serodata <- prepare_serodata(chagas2012)
 #'  seromodel_object <- run_seromodel(
@@ -304,7 +290,6 @@ plot_rhats <- function(seromodel_object,
 #'    n_iters = 1000
 #'  )
 #' plot_seromodel(seromodel_object, size_text = 15)
-#' }
 #' @export
 plot_seromodel <- function(seromodel_object,
                           max_lambda = NA,
@@ -380,16 +365,15 @@ plot_seromodel <- function(seromodel_object,
 #' @param size_text Text size of the graph returned by the function
 #' @return p the plot for the given table
 #' @examples
-#' \dontrun{
-#'  serodata <- prepare_serodata(chagas2012)
-#'  seromodel_object <- run_seromodel(
-#'    serodata = serodata,
-#'    foi_model = "constant",
-#'    n_iters = 1000
-#'  )
-#' info = t(seromodel_object$model_summary)
+#' serodata <- prepare_serodata(chagas2012)
+#' seromodel_object <- run_seromodel(
+#'   serodata = serodata,
+#'   foi_model = "constant",
+#'   n_iters = 1000
+#' )
+#' seromodel_summary = extract_seromodel_summary(seromodel_object)
+#' info = t(seromodel_summary)
 #' plot_info_table (info, size_text = 15)
-#' }
 #' @export
 plot_info_table <- function(info, size_text) {
   dato <- data.frame(y = NROW(info):seq_len(1),