(v0.8.0.9009) unit test

R/age.R

@@ -133,6 +133,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
 #' # same:
 #' age_groups(ages, c(1, 2, 4, 6, 13, 17))
 #'
+#' \dontrun{
 #' # resistance of ciprofloxacine per age group
 #' library(dplyr)
 #' example_isolates %>%
@@ -141,6 +142,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
 #'   group_by(age_group = age_groups(age)) %>%
 #'   select(age_group, CIP) %>%
 #'   ggplot_rsi(x = "age_group")
+#' }
 age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
   if (!is.numeric(x)) {
     stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".")

R/ggplot_rsi.R

@@ -99,7 +99,9 @@
 #' example_isolates %>%
 #'   select(AMX) %>%
 #'   ggplot_rsi(colours = c(SI = "yellow"))
-#'
+#'   
+#' \dontrun{
+#' 
 #' # resistance of ciprofloxacine per age group
 #' example_isolates %>%
 #'   mutate(first_isolate = first_isolate(.)) %>%
@@ -110,8 +112,7 @@
 #'   select(age_group,
 #'          CIP) %>%
 #'   ggplot_rsi(x = "age_group")
-#' \donttest{
-#'
+#'   
 #' # for colourblind mode, use divergent colours from the viridis package:
 #' example_isolates %>%
 #'   select(AMX, NIT, FOS, TMP, CIP) %>%

R/mdro.R

@@ -25,7 +25,6 @@
 #' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details.
 #' @param info print progress
 #' @inheritParams eucast_rules
-#' @param verbose print additional info: missing antibiotic columns per parameter
 #' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.
 #' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
 #' @inheritSection eucast_rules Antibiotics