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110 lines
4.2 KiB
R
Executable File
110 lines
4.2 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.gitab.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. 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 tbl a \code{data.frame}
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#' @param col a character to look 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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#' @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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#' # using column `tetr` for col "J01AA07"
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#' # [1] "tetr"
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guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
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if (is.null(tbl) & is.null(col)) {
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return(as.name("guess_ab_col"))
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}
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#stop("This function should not be called directly.")
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if (length(col) > 1) {
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warning("argument 'col' has length > 1 and only the first element will be used")
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col <- col[1]
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}
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if (!is.data.frame(tbl)) {
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stop("`tbl` must be a data.frame")
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}
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tbl_names <- colnames(tbl)
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if (col %in% tbl_names) {
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return(col)
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}
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ab_result <- antibiotics %>%
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select(atc:trade_name) %>%
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filter_all(any_vars(tolower(.) == tolower(col))) %>%
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filter_all(any_vars(. %in% tbl_names))
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if (nrow(ab_result) == 0 & nchar(col) > 4) {
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# use like when col >= 5 characters
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ab_result <- antibiotics %>%
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select(atc:trade_name) %>%
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filter_all(any_vars(tolower(.) %like% tolower(col))) %>%
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filter_all(any_vars(. %in% tbl_names))
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}
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if (nrow(ab_result) > 1) {
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# looking more and more for reliable hit
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ab_result_1 <- ab_result %>% filter(tolower(atc) == tolower(col))
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if (nrow(ab_result_1) == 0) {
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ab_result_1 <- ab_result %>% filter(tolower(certe) == tolower(col))
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}
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if (nrow(ab_result_1) == 0) {
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ab_result_1 <- ab_result %>% filter(tolower(umcg) == tolower(col))
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}
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if (nrow(ab_result_1) == 0) {
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ab_result_1 <- ab_result %>% filter(tolower(official) == tolower(col))
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}
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if (nrow(ab_result_1) == 0) {
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ab_result_1 <- ab_result[1, ]
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}
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ab_result <- ab_result_1
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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 result found for col "', col, '"')
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}
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return(NULL)
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} else {
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result <- tbl_names[tbl_names %in% ab_result]
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if (length(result) == 0) {
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if (verbose == TRUE) {
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message('no result found for col "', col, '"')
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}
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return(NULL)
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}
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if (verbose == TRUE) {
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message('using column `', result, '` for col "', col, '"')
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}
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return(result)
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}
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}
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