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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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6
R/ab_property.R
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@ -338,7 +338,7 @@ 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)
meet_criteria(language, is_in = c(LANGUAGES_SUPPORTED, ""), has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
language <- validate_language(language)
translate_into_language(ab_validate(x = x, property = property, ...), language = language)
}
@ -367,7 +367,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
if (!is.null(out)) {
df <- data[, out, drop = FALSE]
} else {
df <- pm_select(data, ...)
df <- select(data, ...)
}
} else {
df <- data
@ -438,7 +438,7 @@ 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