P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 05:41:59 +02:00
Code Releases Activity

sort sir history

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
Download Patch File Download Diff File Expand all files Collapse all files

69
R/ab.R
View File

@ -87,7 +87,6 @@
#'
#' \donttest{
#' if (require("dplyr")) {
#'
#' # you can quickly rename 'sir' columns using set_ab_names() with dplyr:
#' example_isolates %>%
#' set_ab_names(where(is.sir), property = "atc")
@ -338,22 +337,23 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# transform back from other languages and try again
x_translated <- paste(lapply(
strsplit(x[i], "[^A-Z0-9]"),
function(y) {
for (i in seq_len(length(y))) {
for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
!isFALSE(TRANSLATIONS$fixed)), "pattern"],
y[i]
)
x_translated <- paste(
lapply(
strsplit(x[i], "[^A-Z0-9]"),
function(y) {
for (i in seq_len(length(y))) {
for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
!isFALSE(TRANSLATIONS$fixed)), "pattern"],
y[i]
)
}
}
generalise_antibiotic_name(y)
}
generalise_antibiotic_name(y)
}
)[[1]],
collapse = "/"
)[[1]],
collapse = "/"
)
x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
if (!is.na(x_translated_guess)) {
@ -362,20 +362,21 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# now also try to coerce brandname combinations like "Amoxy/clavulanic acid"
x_translated <- paste(lapply(
strsplit(x_translated, "[^A-Z0-9 ]"),
function(y) {
for (i in seq_len(length(y))) {
y_name <- suppressWarnings(ab_name(y[i], language = NULL, initial_search = FALSE))
y[i] <- ifelse(!is.na(y_name),
y_name,
y[i]
)
x_translated <- paste(
lapply(
strsplit(x_translated, "[^A-Z0-9 ]"),
function(y) {
for (i in seq_len(length(y))) {
y_name <- suppressWarnings(ab_name(y[i], language = NULL, initial_search = FALSE))
y[i] <- ifelse(!is.na(y_name),
y_name,
y[i]
)
}
generalise_antibiotic_name(y)
}
generalise_antibiotic_name(y)
}
)[[1]],
collapse = "/"
)[[1]],
collapse = "/"
)
x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
if (!is.na(x_translated_guess)) {
@ -513,8 +514,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
)
}
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
x_unknown <- c(x_unknown,
AMR_env$ab_previously_coerced$x_bak[which(AMR_env$ab_previously_coerced$x %in% x & is.na(AMR_env$ab_previously_coerced$ab))])
x_unknown <- c(
x_unknown,
AMR_env$ab_previously_coerced$x_bak[which(AMR_env$ab_previously_coerced$x %in% x & is.na(AMR_env$ab_previously_coerced$ab))]
)
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
@ -660,9 +663,9 @@ get_translate_ab <- function(translate_ab) {
} else {
translate_ab <- tolower(translate_ab)
stop_ifnot(translate_ab %in% colnames(AMR::antibiotics),
"invalid value for 'translate_ab', this must be a column name of the antibiotics data set\n",
"or TRUE (equals 'name') or FALSE to not translate at all.",
call = FALSE
"invalid value for 'translate_ab', this must be a column name of the antibiotics data set\n",
"or TRUE (equals 'name') or FALSE to not translate at all.",
call = FALSE
)
translate_ab
}