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AMR/R/guess_ab.R

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3.3 KiB
R

# ==================================================================== #
# 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.
#' @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
#
guess_ab <- function(tbl = NULL, col = NULL, verbose = FALSE) {
if (is.null(tbl) & is.null(col)) {
return(as.name("guess_ab"))
}
#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)
ab_result <- antibiotics %>%
select(atc:trade_name) %>%
filter_all(any_vars(tolower(.) == tolower(col)))
if (nrow(ab_result) > 1) {
# get most likely one
if (col %in% ab_result$atc) {
ab_result <- ab_result %>% filter(atc == col)
} else if (col %in% ab_result$certe) {
ab_result <- ab_result %>% filter(certe == col)
} else if (col %in% ab_result$umcg) {
ab_result <- ab_result %>% filter(umcg == col)
} else if (col %in% ab_result$umcg) {
ab_result <- ab_result %>% filter(official == col)
} else {
ab_result <- ab_result[1,]
}
}
tbl_result <- tbl_names[tbl_names %in% ab_result]
if (length(tbl_result) > 1) {
tbl_result <- tbl_result[1]
warning('using column `', tbl_result, '` for col "', col, '"', call. = FALSE)
} else if (length(tbl_result) == 0) {
if (verbose == TRUE) {
message('no result found for col "', col, '"')
}
return(NULL)
} else if (verbose == TRUE) {
message('using column `', tbl_result, '` for col "', col, '"')
}
tbl_result
}