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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.gitab.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 tbl a \code{data.frame}
#' @param col a character to look for
#' @param verbose a logical to indicate whether additional info should be printed
#' @importFrom dplyr %>% select filter_all any_vars
#' @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)
#' # using column `tetr` for col "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.atc("augmentin"))
#' # [1] "AMC_ED20"
guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
if (is.null(tbl) & is.null(col)) {
return(as.name("guess_ab_col"))
}
#stop("This function should not be called directly.")
if (length(col) > 1) {
warning("argument 'col' has length > 1 and only the first element will be used")
col <- col[1]
}
if (!is.data.frame(tbl)) {
stop("`tbl` must be a data.frame")
}
tbl_names <- colnames(tbl)
tbl_names_stripped <- colnames(tbl) %>%
strsplit("_") %>%
lapply(function(x) {x[1]}) %>%
unlist()
if (col %in% tbl_names) {
return(col)
}
ab_result <- antibiotics %>%
select(atc:trade_name) %>%
filter_all(any_vars(tolower(.) == tolower(col))) %>%
filter_all(any_vars(. %in% tbl_names))
if (nrow(ab_result) == 0 & nchar(col) > 4) {
# use like when col >= 5 characters
ab_result <- antibiotics %>%
select(atc:trade_name) %>%
filter_all(any_vars(tolower(.) %like% tolower(col))) %>%
filter_all(any_vars(. %in% tbl_names))
}
# WHONET
if (nrow(ab_result) == 0) {
# use like when col >= 5 characters
ab_result <- antibiotics %>%
select(atc:trade_name) %>%
filter_all(any_vars(tolower(.) == tolower(col))) %>%
filter_all(any_vars(. %in% tbl_names_stripped))
}
if (nrow(ab_result) > 1) {
# looking more and more for reliable hit
ab_result_1 <- ab_result %>% filter(tolower(atc) == tolower(col))
if (nrow(ab_result_1) == 0) {
ab_result_1 <- ab_result %>% filter(tolower(certe) == tolower(col))
}
if (nrow(ab_result_1) == 0) {
ab_result_1 <- ab_result %>% filter(tolower(umcg) == tolower(col))
}
if (nrow(ab_result_1) == 0) {
ab_result_1 <- ab_result %>% filter(tolower(official) == tolower(col))
}
if (nrow(ab_result_1) == 0) {
ab_result_1 <- ab_result[1, ]
}
ab_result <- ab_result_1
}
if (length(ab_result) == 0) {
if (verbose == TRUE) {
message('no result found for col "', col, '"')
}
return(NULL)
} else {
result <- tbl_names[tbl_names %in% ab_result]
if (length(result) == 0) {
result <- tbl_names[tbl_names_stripped %in% ab_result]
}
if (length(result) == 0) {
if (verbose == TRUE) {
message('no result found for col "', col, '"')
}
return(NULL)
}
if (verbose == TRUE) {
message('using column `', result, '` for col "', col, '"')
}
return(result)
}
}