P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 22:41:52 +02:00
Code Releases Activity

revert back to pre-antibiogram

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-09 13:07:39 +01:00
parent aa48c6bf53
commit 1a0dc4bf46
53 changed files with 984 additions and 1996 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
R/ab_property.R
View File

@ -113,7 +113,8 @@
#' set_ab_names(property = "atc")
#'
#' example_isolates %>%
#' set_ab_names(where(is.sir))
#' set_ab_names(where(is.sir)) %>%
#' colnames()
#'
#' example_isolates %>%
#' set_ab_names(NIT:VAN) %>%
@ -334,7 +335,7 @@ ab_url <- function(x, open = FALSE, ...) {
ab_property <- function(x, property = "name", language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, is_in = colnames(AMR::antibiotics), has_length = 1)
language <- validate_language(language)
meet_criteria(language, is_in = c(LANGUAGES_SUPPORTED, ""), has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
translate_into_language(ab_validate(x = x, property = property, ...), language = language)
}
@ -359,7 +360,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
if (is.data.frame(data)) {
if (tryCatch(length(c(...)) > 1, error = function(e) TRUE)) {
df <- tryCatch(suppressWarnings(select(data, ...)),
df <- tryCatch(suppressWarnings(pm_select(data, ...)),
error = function(e) {
data[, c(...), drop = FALSE]
})
@ -434,7 +435,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
ab_validate <- function(x, property, ...) {
if (tryCatch(all(x[!is.na(x)] %in% AMR_env$AB_lookup$ab), error = function(e) FALSE)) {
# # special case for ab_* functions where class is already 'ab'
# special case for ab_* functions where class is already 'ab'
x <- AMR_env$AB_lookup[match(x, AMR_env$AB_lookup$ab), property, drop = TRUE]
} else {
# try to catch an error when inputting an invalid argument