1
0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 00:23:03 +02:00

(v0.7.0.9005) ab algorithm update

This commit is contained in:
2019-06-11 14:18:25 +02:00
parent f6c47c8c88
commit 8f674e19bb
36 changed files with 274 additions and 248 deletions

View File

@ -73,14 +73,13 @@
#' ab_name(21319) # "Flucloxacillin" (using CID)
#' ab_name("J01CF05") # "Flucloxacillin" (using ATC)
ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
x <- ab_validate(x = x, property = "name", ...)
res <- t(x, language = language)
x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
if (tolower == TRUE) {
# use perl to only transform the first character
# as we want "polymyxin B", not "polymyxin b"
res <- gsub("^([A-Z])", "\\L\\1", res, perl = TRUE)
x <- gsub("^([A-Z])", "\\L\\1", x, perl = TRUE)
}
res
x
}
#' @rdname ab_property
@ -116,19 +115,19 @@ ab_tradenames <- function(x, ...) {
#' @rdname ab_property
#' @export
ab_group <- function(x, language = get_locale(), ...) {
t(ab_validate(x = x, property = "group", ...), language = language)
translate_AMR(ab_validate(x = x, property = "group", ...), language = language)
}
#' @rdname ab_property
#' @export
ab_atc_group1 <- function(x, language = get_locale(), ...) {
t(ab_validate(x = x, property = "atc_group1", ...), language = language)
translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language)
}
#' @rdname ab_property
#' @export
ab_atc_group2 <- function(x, language = get_locale(), ...) {
t(ab_validate(x = x, property = "atc_group2", ...), language = language)
translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
}
#' @rdname ab_property
@ -150,8 +149,8 @@ ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
#' @export
ab_info <- function(x, language = get_locale(), ...) {
x <- AMR::as.ab(x, ...)
base::list(ab = x,
atc = ab_atc(x),
base::list(ab = as.character(x),
atc = as.character(ab_atc(x)),
cid = ab_cid(x),
name = ab_name(x, language = language),
group = ab_group(x, language = language),
@ -174,7 +173,7 @@ ab_property <- function(x, property = 'name', language = get_locale(), ...) {
stop("invalid property: '", property, "' - use a column name of the `antibiotics` data set")
}
t(ab_validate(x = x, property = property, ...), language = language)
translate_AMR(ab_validate(x = x, property = property, ...), language = language)
}
ab_validate <- function(x, property, ...) {