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(v1.7.1.9058) vars selection for set_ab_names()

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dr. M.S. (Matthijs) Berends
2021-12-05 22:06:45 +01:00
parent 3abe61fd61
commit 7965468ccd
100 changed files with 5220 additions and 9555 deletions
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16
R/ab_property.R
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@ -33,7 +33,7 @@
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
#' @param administration way of administration, either `"oral"` or `"iv"`
#' @param open browse the URL using [utils::browseURL()]
#' @param ... other arguments passed on to [as.ab()]
#' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: variables to select (supports tidy selection like `AMX:VAN`), otherwise other arguments passed on to [as.ab()]
#' @param data a [data.frame] of which the columns need to be renamed, or a [character] vector of column names
#' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`)
#' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
@ -97,6 +97,7 @@
#' # use set_ab_names() for renaming columns
#' colnames(example_isolates)
#' colnames(set_ab_names(example_isolates))
#' colnames(set_ab_names(example_isolates, NIT:VAN))
#' \donttest{
#' if (require("dplyr")) {
#' example_isolates %>%
@ -109,6 +110,14 @@
#' # set_ab_names() works with any AB property:
#' example_isolates %>%
#' set_ab_names("atc")
#'
#' example_isolates %>%
#' set_ab_names(where(is.rsi)) %>%
#' colnames()
#'
#' example_isolates %>%
#' set_ab_names(NIT:VAN) %>%
#' colnames()
#' }
#' }
ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
@ -328,7 +337,7 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
#' @rdname ab_property
#' @aliases ATC
#' @export
set_ab_names <- function(data, property = "name", language = get_locale(), snake_case = NULL) {
set_ab_names <- function(data, ..., property = "name", language = get_locale(), snake_case = NULL) {
meet_criteria(data, allow_class = c("data.frame", "character"))
meet_criteria(property, is_in = colnames(antibiotics), has_length = 1, ignore.case = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -345,7 +354,8 @@ set_ab_names <- function(data, property = "name", language = get_locale(), snake
}
if (is.data.frame(data)) {
vars <- get_column_abx(data, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
df <- pm_select(data, ...)
vars <- get_column_abx(df, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
if (length(vars) == 0) {
message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
return(data)