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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

98
R/add_custom_antimicrobials.R Normal file
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@ -0,0 +1,98 @@
# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Add Manual Antimicrobials to This Package
#'
#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, for example:
#'
#' ```r
#' library(AMR)
#' add_custom_antimicrobials(
#' data.frame(ab = "TEST",
#' name = "Test Antibiotic",
#' group = "Test Group")
#' )
#' ```
#'
#' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials.
#' @rdname add_custom_antimicrobials
#' @export
#' @examples
#' \donttest{
#'
#' # returns NA and throws a warning:
#' as.ab("test")
#'
#' # now a manual entry - it will be considered by as.ab() and
#' # all ab_*() functions
#' add_custom_antimicrobials(
#' data.frame(ab = "TEST",
#' name = "Test Antibiotic",
#' group = "Test Group")
#' )
#'
#' "test" is now a new antibiotic:
#' as.ab("test")
#' ab_name("test")
#' ab_group("test")
#' }
add_custom_antimicrobials <- function(x) {
meet_criteria(x, allow_class = "data.frame")
stop_ifnot(all(c("ab", "name") %in% colnames(x)),
"`x` must contain columns \"ab\" and \"name\".")
stop_if(any(x$ab %in% AB_lookup$ab),
"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AB_lookup$ab]), " already exist in the internal `antibiotics` data set.")
x <- x[, colnames(AB_lookup)[colnames(AB_lookup) %in% colnames(x)], drop = FALSE]
x$generalised_name <- generalise_antibiotic_name(x$name)
x$generalised_all <- as.list(x$generalised_name)
bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
if (!is.null(bind_rows)) {
new_df <- bind_rows(AB_lookup, x)
} else {
new_df <- rbind(AB_lookup, x, stringsAsFactors = FALSE)
}
assignInNamespace(x = "AB_lookup",
value = new_df,
ns = asNamespace("AMR"))
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to internal `antibiotics` data set.")
}
#' @rdname add_custom_antimicrobials
#' @export
clear_custom_antimicrobials <- function() {
assignInNamespace(x = "AB_lookup",
value = create_AB_lookup(),
ns = asNamespace("AMR"))
message_("Manual antimicrobials cleared.")
}