mirror of https://github.com/msberends/AMR.git
93 lines
4.0 KiB
R
Executable File
93 lines
4.0 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Guess antibiotic column
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#'
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#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
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#' @param x a \code{data.frame}
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#' @param search_string a text to search \code{x} for
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#' @param verbose a logical to indicate whether additional info should be printed
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#' @importFrom dplyr %>% select filter_all any_vars
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#' @importFrom crayon blue
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#' @return A column name of \code{x}, or \code{NULL} when no result is found.
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' df <- data.frame(amox = "S",
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#' tetr = "R")
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#'
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#' guess_ab_col(df, "amoxicillin")
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#' # [1] "amox"
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#' guess_ab_col(df, "J01AA07") # ATC code of tetracycline
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#' # [1] "tetr"
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#'
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#' guess_ab_col(df, "J01AA07", verbose = TRUE)
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#' # Note: Using column `tetr` as input for "J01AA07".
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#' # [1] "tetr"
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#'
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#' # WHONET codes
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#' df <- data.frame(AMP_ND10 = "R",
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#' AMC_ED20 = "S")
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#' guess_ab_col(df, "ampicillin")
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#' # [1] "AMP_ND10"
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#' guess_ab_col(df, "J01CR02")
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#' # [1] "AMC_ED20"
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#' guess_ab_col(df, as.ab("augmentin"))
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#' # [1] "AMC_ED20"
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guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
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if (is.null(x) & is.null(search_string)) {
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return(as.name("guess_ab_col"))
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}
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if (length(search_string) > 1) {
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warning("argument 'search_string' has length > 1 and only the first element will be used")
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search_string <- search_string[1]
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}
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search_string <- as.character(search_string)
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if (!is.data.frame(x)) {
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stop("`x` must be a data.frame")
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}
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if (search_string %in% colnames(x)) {
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ab_result <- search_string
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} else {
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# sort colnames on length - longest first
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cols <- colnames(x[, x %>% colnames() %>% nchar() %>% order() %>% rev()])
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df_trans <- data.frame(cols = cols,
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abs = suppressWarnings(as.ab(cols)),
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stringsAsFactors = FALSE)
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ab_result <- df_trans[which(df_trans$abs == as.ab(search_string)), "cols"]
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ab_result <- ab_result[!is.na(ab_result)][1L]
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}
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if (length(ab_result) == 0) {
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if (verbose == TRUE) {
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message('No column found as input for `', search_string, '`.')
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}
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return(NULL)
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} else {
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if (verbose == TRUE) {
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message(blue(paste0("NOTE: Using column `", bold(ab_result), "` as input for `", search_string, "`.")))
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}
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return(ab_result)
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}
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}
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