(v1.3.0) skip more CRAN tests

R/ab_class_selectors.R

@@ -31,7 +31,8 @@
 #' @name antibiotic_class_selectors
 #' @export
 #' @examples 
-#' if (require("dplyr")) {
+#' \dontrun{
+#'   library(dplyr)
 #' 
 #'   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
 #'   example_isolates %>% 

R/ab_from_text.R

@@ -64,7 +64,7 @@
 #' abx <- ab_from_text("500 mg amoxi po and 400mg cipro iv")
 #' ab_group(abx[[1]])
 #' 
-#' if (require(dplyr)) {
+#' if (require("dplyr")) {
 #'   tibble(clinical_text = c("given 400mg cipro and 500 mg amox",
 #'                            "started on doxy iv today")) %>% 
 #'     mutate(abx_codes = ab_from_text(clinical_text),

R/filter_ab_class.R

@@ -33,7 +33,8 @@
 #' @seealso [antibiotic_class_selectors()] for the `select()` equivalent.
 #' @export
 #' @examples
-#' if (require(dplyr)) {
+#' \dontrun{
+#' library(dplyr)
 #'
 #' # filter on isolates that have any result for any aminoglycoside
 #' example_isolates %>% filter_ab_class("aminoglycoside")
@@ -62,9 +63,7 @@
 #' example_isolates %>%
 #'   filter_aminoglycosides("R", "all") %>%
 #'   filter_fluoroquinolones("R", "all")
-#' }
 #' 
-#' \dontrun{
 #' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
 #' example_isolates %>% filter_carbapenems("R", "all")
 #' example_isolates %>% filter(across(carbapenems(), ~. == "R"))

R/ggplot_pca.R

@@ -60,7 +60,8 @@
 #' # See ?example_isolates.
 #'
 #' # See ?pca for more info about Principal Component Analysis (PCA).
-#' if (require("dplyr")) {
+#' \dontrun{
+#'   library(dplyr)
 #'   pca_model <- example_isolates %>% 
 #'     filter(mo_genus(mo) == "Staphylococcus") %>% 
 #'     group_by(species = mo_shortname(mo)) %>%

R/resistance_predict.R

@@ -84,7 +84,9 @@
 #' }
 #'
 #' # create nice plots with ggplot2 yourself
-#' if (require(ggplot2) & require("dplyr")) {
+#' \dontrun{
+#'   library(dplyr)
+#'   library(ggplot2)
 #'
 #'   data <- example_isolates %>%
 #'     filter(mo == as.mo("E. coli")) %>%