fix: replace run_seromodel by fit_seromodel in examples and vignettes

Author: ntorresd

R/model_comparison.R

@@ -9,7 +9,7 @@
 #' @examples
 #' data(chagas2012)
 #' serodata <- prepare_serodata(serodata = chagas2012)
-#' model_constant <- run_seromodel(
+#' model_constant <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant",
 #'   iter = 1500

R/modelling.R

@@ -137,12 +137,14 @@ validate_prepared_serodata <- function(serodata) {
 #'   the implementation of the model. For further details refer to
 #'   [fit_seromodel].
 #' @examples
+#' \dontrun{
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
 #' run_seromodel(
 #'   serodata,
 #'   foi_model = "constant"
 #' )
+#' }
 #' @export
 run_seromodel <- function(
     serodata,
@@ -512,7 +514,7 @@ get_foi_central_estimates <- function(seromodel_object,
 #' @examples
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
+#' seromodel_object <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant"
 #' )
@@ -587,7 +589,7 @@ extract_seromodel_summary <- function(seromodel_object,
 #' @examples
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
+#' seromodel_object <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant"
 #' )

R/visualisation.R

@@ -87,7 +87,7 @@ plot_seroprev <- function(serodata,
 #' @examples
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
+#' seromodel_object <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant",
 #'   iter = 1000
@@ -173,7 +173,7 @@ plot_seroprev_fitted <- function(seromodel_object,
 #' @examples
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
+#' seromodel_object <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant",
 #'   iter = 1000
@@ -267,7 +267,7 @@ plot_foi <- function(seromodel_object,
 #' @examples
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
+#' seromodel_object <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant",
 #'   iter = 1000
@@ -343,7 +343,7 @@ plot_rhats <- function(seromodel_object,
 #' @examples
 #' data(chagas2012)
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
+#' seromodel_object <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant",
 #'   iter = 1000
@@ -421,7 +421,7 @@ plot_seromodel <- function(seromodel_object,
 #' @return ggplot object summarizing the information in `info_table`
 #' @examples
 #' serodata <- prepare_serodata(chagas2012)
-#' seromodel_object <- run_seromodel(
+#' seromodel_object <- fit_seromodel(
 #'   serodata = serodata,
 #'   foi_model = "constant",
 #'   iter = 1000