AMR/R/guess_ab_col.R

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