P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 02:03:04 +02:00
Code Releases Activity

(v0.9.0.9023) EUCAST 2020 guidelines

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-02-14 19:54:13 +01:00
parent 5a98e6b777
commit 9b8b02960e
43 changed files with 16588 additions and 14564 deletions
Download Patch File Download Diff File Expand all files Collapse all files

15
R/ab_property.R
View File

@ -168,7 +168,7 @@ ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
#' @rdname ab_property
#' @export
ab_info <- function(x, language = get_locale(), ...) {
x <- AMR::as.ab(x, ...)
x <- as.ab(x, ...)
base::list(ab = as.character(x),
atc = ab_atc(x),
cid = ab_cid(x),
@ -189,7 +189,7 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
if (length(property) != 1L) {
stop("'property' must be of length 1.")
}
if (!property %in% colnames(AMR::antibiotics)) {
if (!property %in% colnames(antibiotics)) {
stop("invalid property: '", property, "' - use a column name of the `antibiotics` data set")
}
@ -197,14 +197,17 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
}
ab_validate <- function(x, property, ...) {
check_dataset_integrity()
# try to catch an error when inputting an invalid parameter
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% AMR::antibiotics[1, property],
tryCatch(x[1L] %in% antibiotics[1, property],
error = function(e) stop(e$message, call. = FALSE))
x_bak <- x
if (!all(x %in% AMR::antibiotics[, property])) {
x <- data.frame(ab = AMR::as.ab(x, ...), stringsAsFactors = FALSE) %>%
left_join(AMR::antibiotics, by = "ab") %>%
if (!all(x %in% antibiotics[, property])) {
x <- data.frame(ab = as.ab(x, ...), stringsAsFactors = FALSE) %>%
left_join(antibiotics, by = "ab") %>%
pull(property)
}
if (property == "ab") {