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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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10
R/ab.R
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@ -32,7 +32,7 @@
#' Use this function to determine the antibiotic drug code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
#' @param x a [character] vector to determine to antibiotic ID
#' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antibiotic drug code or name can be retrieved from a single input value.
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param info a [logical] to indicate whether a progress bar should be printed - the default is `TRUE` only in interactive mode
#' @param ... arguments passed on to internal functions
#' @rdname as.ab
#' @inheritSection WHOCC WHOCC
@ -133,11 +133,11 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
note_if_more_than_one_found <- function(found, index, from_text) {
if (isTRUE(initial_search) && isTRUE(length(from_text) > 1)) {
abnames <- ab_name(from_text, tolower = TRUE, initial_search = FALSE)
if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|avibactam)") {
abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam")]
if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|(avi|tazo|mono|vabor)bactam)") {
abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam", "tazobactam", "vaborbactam", "monobactam")]
}
if (length(abnames) > 1) {
warning_(
message_(
"More than one result was found for item ", index, ": ",
vector_and(abnames, quotes = FALSE)
)
@ -248,6 +248,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
print("here")
# length of input is quite long, and Levenshtein distance is only max 2
if (nchar(x[i]) >= 10) {