Remove serodata from pre-loaded datasets of the package (#107)

* remove serodata .Rdata and .Rd files

* remove R/serodata.R

* doc: update functions  documentation replacing  for  in examples

* doc: update serofoi logo

* doc: update README and vignettes
This commit changes the removed preloaded dataset `serodata` for the identical `chagas2012`.

* fix: minor correction to test_modelling

R/model_comparison.R

@@ -7,18 +7,14 @@
 #' @inheritParams get_foi_central_estimates
 #' @return rhats table
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
-#' serodata <- prepare_serodata(serodata = chagas2012)
-#' model_constant <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant",
-#'   iter = 1500
-#' )
-#' cohort_ages <- get_cohort_ages(serodata)
-#' get_table_rhats(
-#'   seromodel_object = model_constant,
-#'   cohort_ages = cohort_ages
-#' )
+#' 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)
+#' }
 #' @export
 get_table_rhats <- function(seromodel_object,
                             cohort_ages) {

R/modelling.R

@@ -124,12 +124,11 @@ validate_prepared_serodata <- function(serodata) {
 #'   the implementation of the model. For further details refer to
 #'   [fit_seromodel].
 #' @examples
-#' data(chagas2012)
+#' \dontrun{
 #' serodata <- prepare_serodata(chagas2012)
-#' run_seromodel(
-#'   serodata,
-#'   foi_model = "constant"
-#' )
+#' run_seromodel (chagas2012,
+#'                foi_model = "constant")
+#' }
 #' @export
 run_seromodel <- function(
     serodata,
@@ -220,12 +219,12 @@ run_seromodel <- function(
 #' @return `seromodel_object`. `stanfit` object returned by the function
 #'   [sampling][rstan::sampling]
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_fit <- fit_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant"
-#' )
+#' seromodel_fit <- fit_seromodel(serodata = serodata,
+#'                                foi_model = "constant")
+#' }
 #'
 #' @export
 fit_seromodel <- function(
@@ -317,9 +316,11 @@ fit_seromodel <- function(
 #' @return `cohort_ages`. A data.frame containing the age of each cohort
 #'   corresponding to each birth year
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(serodata = chagas2012, alpha = 0.05)
-#' cohort_ages <- get_cohort_ages(serodata = serodata)
+#' exposure_ages <- get_exposure_ages(serodata)
+#' }
 #' @export
 get_cohort_ages <- function(serodata) {
   birth_year <- (min(serodata$birth_year):serodata$tsur[1])
@@ -341,6 +342,7 @@ get_cohort_ages <- function(serodata) {
 #' @return `exposure_output`. An atomic matrix containing the expositions for
 #'   each entry of `serodata` by year.
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(serodata = chagas2012)
 #' exposure_matrix <- get_exposure_matrix(serodata = serodata)
@@ -429,15 +431,13 @@ get_foi_central_estimates <- function(seromodel_object,
 #'   \item{`converged`}{convergence}
 #' }
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant"
-#' )
-#' extract_seromodel_summary(seromodel_object,
-#'   serodata = serodata
-#' )
+#' seromodel_object <- run_seromodel(serodata = serodata,
+#'                                   foi_model = "constant")
+#' extract_seromodel_summary(seromodel_object)
+#' }
 #' @export
 extract_seromodel_summary <- function(seromodel_object,
                                       serodata) {
@@ -503,14 +503,14 @@ extract_seromodel_summary <- function(seromodel_object,
 #' @return `prev_final`. The expanded prevalence data. This is used for plotting
 #'   purposes in the `visualization` module.
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant"
-#' )
-#' foi <- rstan::extract(seromodel_object, "foi")[[1]]
-#' get_prev_expanded(foi, serodata)
+#' seromodel_object <- run_seromodel(serodata = serodata,
+#'                           foi_model = "constant")
+#' foi <- rstan::extract(seromodel_object$fit, "foi")[[1]]
+#' get_prev_expanded <- function(foi, serodata)
+#' }
 #' @export
 get_prev_expanded <- function(foi,
                               serodata,

R/seroprevalence_data.R

@@ -39,8 +39,10 @@
 #'     observed prevalence}
 #' }
 #' @examples
+#'\dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
+#' }
 #' @export
 prepare_serodata <- function(serodata = serodata,
                              alpha = 0.05) {
@@ -93,11 +95,11 @@ prepare_serodata <- function(serodata = serodata,
 #' @inheritParams run_seromodel
 #' @return data set with the binomial confidence intervals
 #' @examples
+#'\dontrun{
 #' data(chagas2012)
-#' serodata <- prepare_serodata(chagas2012)
-#' prepare_bin_data(serodata)
-#' @keywords internal
-#' @noRd
+#' prepare_bin_data(chagas2012)
+#' }
+#' @export
 prepare_bin_data <- function(serodata) {
   if (!any(colnames(serodata) == "age_mean_f")) {
     serodata <- serodata %>%

R/visualisation.R

@@ -8,9 +8,16 @@
 #'   data of a given seroprevalence survey with its corresponding binomial
 #'   confidence interval.
 #' @examples
-#' data(chagas2012)
-#' serodata <- prepare_serodata(chagas2012)
-#' plot_seroprev(serodata, size_text = 15)
+#' \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)
+#' }
 #' @export
 plot_seroprev <- function(serodata,
                           size_text = 6) {
@@ -48,17 +55,14 @@ plot_seroprev <- function(serodata,
 #' @return A ggplot object containing the seropositivity-vs-age graph including
 #'   the data, the fitted model and their corresponding confidence intervals.
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant",
-#'   iter = 1000
-#' )
-#' plot_seroprev_fitted(seromodel_object,
-#'   serodata = serodata,
-#'   size_text = 15
-#' )
+#' 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,
                                  serodata,
@@ -148,19 +152,16 @@ plot_seroprev_fitted <- function(seromodel_object,
 #' @return A ggplot2 object containing the Force-of-infection-vs-time including
 #'   the corresponding confidence interval.
 #' @examples
-#' data(chagas2012)
-#' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant",
-#'   iter = 1000
-#' )
-#' cohort_ages <- get_cohort_ages(serodata)
-#' plot_foi(
-#'   seromodel_object = seromodel_object,
-#'   cohort_ages = cohort_ages,
-#'   size_text = 15
-#' )
+#' \dontrun{
+#'  data(chagas2012)
+#'  serodata <- prepare_serodata(chagas2012)
+#'  seromodel_object <- run_seromodel(
+#'    serodata = serodata,
+#'    foi_model = "constant",
+#'    n_iters = 1000
+#'  )
+#' plot_foi(seromodel_object, size_text = 15)
+#' }
 #' @export
 plot_foi <- function(seromodel_object,
                      cohort_ages,
@@ -266,18 +267,17 @@ plot_foi <- function(seromodel_object,
 #'   function.
 #' @return The rhats-convergence plot of the selected model.
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' seromodel_object <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant",
-#'   iter = 1000
-#' )
-#' cohort_ages <- get_cohort_ages(serodata = serodata)
+#'  serodata = serodata,
+#'  foi_model = "constant",
+#'  n_iters = 1000
+#'  )
 #' plot_rhats(seromodel_object,
-#'   cohort_ages = cohort_ages,
-#'   size_text = 15
-#' )
+#'            size_text = 15)
+#' }
 #' @export
 plot_rhats <- function(seromodel_object,
                        cohort_ages,
@@ -344,17 +344,16 @@ plot_rhats <- function(seromodel_object,
 #' @return A ggplot object with a vertical arrange containing the
 #'   seropositivity, force of infection, and convergence plots.
 #' @examples
-#' data(chagas2012)
-#' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant",
-#'   iter = 1000
-#' )
-#' plot_seromodel(seromodel_object,
-#'   serodata = serodata,
-#'   size_text = 15
-#' )
+#' \dontrun{
+#'  data(chagas2012)
+#'  serodata <- prepare_serodata(chagas2012)
+#'  seromodel_object <- run_seromodel(
+#'    serodata = serodata,
+#'    foi_model = "constant",
+#'    n_iters = 1000
+#'  )
+#' plot_seromodel(seromodel_object, size_text = 15)
+#' }
 #' @export
 plot_seromodel <- function(seromodel_object,
                            serodata,
@@ -451,18 +450,16 @@ 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
-#' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
-#'   serodata = serodata,
-#'   foi_model = "constant",
-#'   iter = 1000
-#' )
-#' seromodel_summary <- extract_seromodel_summary(
-#'   seromodel_object = seromodel_object,
-#'   serodata = serodata
-#' )
-#' info <- t(seromodel_summary)
-#' plot_info_table(info, size_text = 15)
+#' \dontrun{
+#'  serodata <- prepare_serodata(chagas2012)
+#'  seromodel_object <- run_seromodel(
+#'    serodata = serodata,
+#'    foi_model = "constant",
+#'    n_iters = 1000
+#'  )
+#' info = t(seromodel_object$model_summary)
+#' plot_info_table (info, size_text = 15)
+#' }
 #' @export
 plot_info_table <- function(info, size_text) {
   dato <- data.frame(