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add add_custom_antimicrobials()

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dr. M.S. (Matthijs) Berends
2022-10-10 20:20:39 +02:00
parent 4fe90092c7
commit 82e3198315
8 changed files with 209 additions and 11 deletions
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20
R/ab.R
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@ -48,6 +48,8 @@
#' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see *Examples*.
#'
#' Note: the [as.ab()] and [`ab_*`][ab_property()] functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
#'
#' You can add your own manual codes to be considered by [as.ab()] and all [`ab_*`][ab_property()] functions, see [add_custom_antimicrobials()].
#' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
#'
@ -218,7 +220,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_loinc,
function(s) x[i] %in% s
))
found <- AMR::antibiotics$ab[loinc_found == TRUE]
found <- AB_lookup$ab[loinc_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -229,7 +231,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_synonyms,
function(s) x[i] %in% s
))
found <- AMR::antibiotics$ab[synonym_found == TRUE]
found <- AB_lookup$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -241,7 +243,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# require at least 2 characters for abbreviations
function(s) x[i] %in% s && nchar(x[i]) >= 2
))
found <- AMR::antibiotics$ab[abbr_found == TRUE]
found <- AB_lookup$ab[abbr_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -288,13 +290,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# try if name starts with it
found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# try if name ends with it
found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
if (nchar(x[i]) >= 4 && length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -305,7 +307,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_synonyms,
function(s) any(s %like% paste0("^", x_spelling))
))
found <- AMR::antibiotics$ab[synonym_found == TRUE]
found <- AB_lookup$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -583,7 +585,7 @@ as.data.frame.ab <- function(x, ...) {
"[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
}
#' @method [[<- ab
#' @export
@ -591,7 +593,7 @@ as.data.frame.ab <- function(x, ...) {
"[[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
}
#' @method c ab
#' @export
@ -600,7 +602,7 @@ c.ab <- function(...) {
x <- list(...)[[1L]]
y <- NextMethod()
attributes(y) <- attributes(x)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
}
#' @method unique ab