(v2.1.1.9050) vctrs fix for sir, small documentation fixes

R/ab_selectors.R

@@ -57,59 +57,31 @@
 #' example_isolates
 #'
 #'
-#' # Examples sections below are split into 'base R', 'dplyr', and 'data.table':
-#'
-#'
-#' # base R ------------------------------------------------------------------
-#'
-#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
-#' example_isolates[, carbapenems()]
-#'
-#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-#' example_isolates[, c("mo", aminoglycosides())]
-#'
-#' # select only antibiotic columns with DDDs for oral treatment
-#' example_isolates[, administrable_per_os()]
-#'
-#' # filter using any() or all()
-#' example_isolates[any(carbapenems() == "R"), ]
-#' subset(example_isolates, any(carbapenems() == "R"))
-#'
-#' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
-#' example_isolates[any(carbapenems()), ]
-#' example_isolates[all(carbapenems()), ]
-#'
-#' # filter with multiple antibiotic selectors using c()
-#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
-#'
-#' # filter + select in one go: get penicillins in carbapenem-resistant strains
-#' example_isolates[any(carbapenems() == "R"), penicillins()]
-#'
-#' # You can combine selectors with '&' to be more specific. For example,
-#' # penicillins() would select benzylpenicillin ('peni G') and
-#' # administrable_per_os() would select erythromycin. Yet, when combined these
-#' # drugs are both omitted since benzylpenicillin is not administrable per os
-#' # and erythromycin is not a penicillin:
-#' example_isolates[, penicillins() & administrable_per_os()]
-#'
-#' # ab_selector() applies a filter in the `antibiotics` data set and is thus
-#' # very flexible. For instance, to select antibiotic columns with an oral DDD
-#' # of at least 1 gram:
-#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
-#'
+#' # Examples sections below are split into 'dplyr', 'base R', and 'data.table':
+#' 
 #' \donttest{
 #' # dplyr -------------------------------------------------------------------
+#' 
+#' if (require("dplyr")) {
+#'.  example_isolates %>% select(carbapenems())
+#' }
 #'
 #' if (require("dplyr")) {
-#'   tibble(kefzol = random_sir(5)) %>%
-#'     select(cephalosporins())
+#'   # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
+#'   example_isolates %>% select(mo, aminoglycosides())
+#' }
+#'
+#' if (require("dplyr")) {
+#'   # select only antibiotic columns with DDDs for oral treatment
+#'.  example_isolates %>% select(administrable_per_os())
 #' }
 #'
 #' if (require("dplyr")) {
 #'   # get AMR for all aminoglycosides e.g., per ward:
 #'   example_isolates %>%
 #'     group_by(ward) %>%
-#'     summarise(across(aminoglycosides(), resistance))
+#'     summarise(across(aminoglycosides(),
+#'                      resistance))
 #' }
 #' if (require("dplyr")) {
 #'   # You can combine selectors with '&' to be more specific:
@@ -121,7 +93,8 @@
 #'   example_isolates %>%
 #'     filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
 #'     group_by(ward) %>%
-#'     summarise(across(not_intrinsic_resistant(), resistance))
+#'     summarise_at(not_intrinsic_resistant(),
+#'                  resistance)
 #' }
 #' if (require("dplyr")) {
 #'   # get susceptibility for antibiotics whose name contains "trim":
@@ -187,6 +160,44 @@
 #' }
 #'
 #'
+#' # base R ------------------------------------------------------------------
+#'
+#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
+#' example_isolates[, carbapenems()]
+#'
+#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
+#' example_isolates[, c("mo", aminoglycosides())]
+#'
+#' # select only antibiotic columns with DDDs for oral treatment
+#' example_isolates[, administrable_per_os()]
+#'
+#' # filter using any() or all()
+#' example_isolates[any(carbapenems() == "R"), ]
+#' subset(example_isolates, any(carbapenems() == "R"))
+#'
+#' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
+#' example_isolates[any(carbapenems()), ]
+#' example_isolates[all(carbapenems()), ]
+#'
+#' # filter with multiple antibiotic selectors using c()
+#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
+#'
+#' # filter + select in one go: get penicillins in carbapenem-resistant strains
+#' example_isolates[any(carbapenems() == "R"), penicillins()]
+#'
+#' # You can combine selectors with '&' to be more specific. For example,
+#' # penicillins() would select benzylpenicillin ('peni G') and
+#' # administrable_per_os() would select erythromycin. Yet, when combined these
+#' # drugs are both omitted since benzylpenicillin is not administrable per os
+#' # and erythromycin is not a penicillin:
+#' example_isolates[, penicillins() & administrable_per_os()]
+#'
+#' # ab_selector() applies a filter in the `antibiotics` data set and is thus
+#' # very flexible. For instance, to select antibiotic columns with an oral DDD
+#' # of at least 1 gram:
+#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
+#'
+#'
 #' # data.table --------------------------------------------------------------
 #'
 #' # data.table is supported as well, just use it in the same way as with
@@ -679,6 +690,16 @@ ab_select_exec <- function(function_name,
   )
 }
 
+#' @method print ab_selector
+#' @export
+#' @noRd
+print.ab_selector <- function(x, ...) {
+  warning_("It should never be needed to print an antibiotic selector class. Are you using data.table? Then add the argument `with = FALSE`, see our examples at `?ab_selector`.",
+           immediate = TRUE)
+  cat("Class 'ab_selector'\n")
+  print(as.character(x), quote = FALSE)
+}
+
 #' @method c ab_selector
 #' @export
 #' @noRd