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145 lines
6.1 KiB
R
145 lines
6.1 KiB
R
# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Add Custom Antimicrobials to This Package
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#'
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#' With [add_custom_antimicrobials()] you can add your own custom antimicrobial codes to the `AMR` package.
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#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
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#' @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, although this requires to load the `AMR` package at every start-up:
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#'
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#' ```r
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#' # Open .Rprofile file
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#' utils::file.edit("~/.Rprofile")
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#'
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#' # Add custom antibiotic codes:
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#' library(AMR)
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#' add_custom_antimicrobials(
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#' data.frame(ab = "TEST",
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#' name = "Test Antibiotic",
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#' group = "Test Group")
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#' )
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#' ```
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#'
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#' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials.
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#' @rdname add_custom_antimicrobials
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#' @export
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#' @examples
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#' \donttest{
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#'
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#' # returns NA and throws a warning (which is now suppressed):
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#' suppressWarnings(
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#' as.ab("test")
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#' )
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#'
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#' # now add a custom entry - it will be considered by as.ab() and
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#' # all ab_*() functions
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#' add_custom_antimicrobials(
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#' data.frame(ab = "TEST",
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#' name = "Test Antibiotic",
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#' # you can add any property present in the
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#' # 'antibiotics' data set, such as 'group':
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#' group = "Test Group")
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#' )
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#'
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#' # "test" is now a new antibiotic:
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#' as.ab("test")
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#' ab_name("test")
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#' ab_group("test")
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#'
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#' ab_info("test")
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#'
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#'
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#' # Add Co-fluampicil, which is one of the many J01CR50 codes, see
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#' # https://www.whocc.no/ddd/list_of_ddds_combined_products/
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#' add_custom_antimicrobials(
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#' data.frame(ab = "COFLU",
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#' name = "Co-fluampicil",
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#' atc = "J01CR50",
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#' group = "Beta-lactams/penicillines")
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#' )
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#' ab_atc("Co-fluampicil")
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#' ab_name("J01CR50")
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#'
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#' # even antibiotic selectors work
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#' x <- data.frame(random_column = "test",
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#' coflu = as.rsi("S"),
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#' ampicillin = as.rsi("R"))
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#' x
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#' x[, betalactams()]
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#' }
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add_custom_antimicrobials <- function(x) {
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meet_criteria(x, allow_class = "data.frame")
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stop_ifnot(all(c("ab", "name") %in% colnames(x)),
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"`x` must contain columns \"ab\" and \"name\".")
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stop_if(any(x$ab %in% AMR_env$AB_lookup$ab),
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"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AMR_env$AB_lookup$ab]), " already exist in the internal `antibiotics` data set.")
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x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE]
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x$generalised_name <- generalise_antibiotic_name(x$name)
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x$generalised_all <- as.list(x$generalised_name)
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if ("atc" %in% colnames(x)) {
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x$atc <- as.list(x$atc)
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}
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if ("loinc" %in% colnames(x)) {
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x$loinc <- as.list(x$loinc)
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}
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AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
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class(AMR_env$AB_lookup$ab) <- "character"
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bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
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if (is.null(bind_rows)) {
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# do the binding in base R
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new_df <- AMR_env$AB_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
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rownames(new_df) <- NULL
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list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
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for (l in which(list_cols)) {
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# prevent binding NULLs in lists, replace with NA
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new_df[, l] <- as.list(NA_character_)
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}
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for (col in colnames(x)) {
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# assign new values
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new_df[, col] <- x[, col, drop = TRUE]
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}
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AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
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} else {
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# otherwise use dplyr
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AMR_env$AB_lookup <- unique(bind_rows(AMR_env$AB_lookup, x))
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}
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class(AMR_env$AB_lookup$ab) <- c("ab", "character")
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message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
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}
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#' @rdname add_custom_antimicrobials
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#' @export
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clear_custom_antimicrobials <- function() {
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AMR_env$AB_lookup <- create_AB_lookup()
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AMR_env$custom_ab_codes <- character(0)
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message_("Custom antimicrobials cleared.")
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}
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