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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
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68
R/av.R
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@ -308,22 +308,23 @@ as.av <- 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.av(x_translated, initial_search = FALSE))
if (!is.na(x_translated_guess)) {
@ -332,20 +333,21 @@ as.av <- 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(av_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(av_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.av(x_translated, initial_search = FALSE))
if (!is.na(x_translated_guess)) {
@ -478,8 +480,10 @@ as.av <- 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$av_previously_coerced$x_bak[which(AMR_env$av_previously_coerced$x %in% x & is.na(AMR_env$av_previously_coerced$av))])
x_unknown <- c(
x_unknown,
AMR_env$av_previously_coerced$x_bak[which(AMR_env$av_previously_coerced$x %in% x & is.na(AMR_env$av_previously_coerced$av))]
)
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.av()`: these values could not be coerced to a valid antiviral drug ID: ",
@ -604,9 +608,9 @@ get_translate_av <- function(translate_av) {
} else {
translate_av <- tolower(translate_av)
stop_ifnot(translate_av %in% colnames(AMR::antivirals),
"invalid value for 'translate_av', this must be a column name of the antivirals data set\n",
"or TRUE (equals 'name') or FALSE to not translate at all.",
call = FALSE
"invalid value for 'translate_av', this must be a column name of the antivirals data set\n",
"or TRUE (equals 'name') or FALSE to not translate at all.",
call = FALSE
)
translate_av
}