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expert rules 12.0

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dr. M.S. (Matthijs) Berends
2022-11-14 15:20:39 +01:00
parent 7ca44fb756
commit f6862a139d
35 changed files with 433 additions and 128 deletions
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12
R/av.R
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@ -114,7 +114,7 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_unknown_ATCs <- character(0)
note_if_more_than_one_found <- function(found, index, from_text) {
if (initial_search == TRUE && isTRUE(length(from_text) > 1)) {
if (isTRUE(initial_search) && isTRUE(length(from_text) > 1)) {
avnames <- av_name(from_text, tolower = TRUE, initial_search = FALSE)
if (av_name(found[1L], language = NULL) %like% "(clavulanic acid|avibactam)") {
avnames <- avnames[!avnames %in% c("clavulanic acid", "avibactam")]
@ -157,13 +157,13 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_new[is.na(x)] <- NA
already_known[is.na(x)] <- FALSE
if (initial_search == TRUE && sum(already_known) < length(x)) {
if (isTRUE(initial_search) && sum(already_known) < length(x)) {
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
on.exit(close(progress))
}
for (i in which(!already_known)) {
if (initial_search == TRUE) {
if (isTRUE(initial_search)) {
progress$tick()
}
@ -286,7 +286,7 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# INITIAL SEARCH - More uncertain results ----
if (initial_search == TRUE && fast_mode == FALSE) {
if (isTRUE(initial_search) && fast_mode == FALSE) {
# only run on first try
# try by removing all spaces
@ -452,12 +452,12 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
}
if (initial_search == TRUE && sum(already_known) < length(x)) {
if (isTRUE(initial_search) && sum(already_known) < length(x)) {
close(progress)
}
# save to package env to save time for next time
if (initial_search == TRUE) {
if (isTRUE(initial_search)) {
AMR_env$av_previously_coerced <- AMR_env$av_previously_coerced[which(!AMR_env$av_previously_coerced$x %in% x), , drop = FALSE]
AMR_env$av_previously_coerced <- unique(rbind(AMR_env$av_previously_coerced,
data.frame(