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dr. M.S. (Matthijs) Berends
2019-05-13 10:10:16 +02:00
parent 0444c4ed9d
commit 38a4421450
36 changed files with 475 additions and 213 deletions
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35
R/guess_ab_col.R
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@ -22,11 +22,12 @@
#' 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 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
@ -39,7 +40,7 @@
#' # [1] "tetr"
#'
#' guess_ab_col(df, "J01AA07", verbose = TRUE)
#' # using column `tetr` for col "J01AA07"
#' # Note: Using column `tetr` as input for "J01AA07".
#' # [1] "tetr"
#'
#' # WHONET codes
@ -51,40 +52,40 @@
#' # [1] "AMC_ED20"
#' guess_ab_col(df, as.ab("augmentin"))
#' # [1] "AMC_ED20"
guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
if (is.null(tbl) & is.null(col)) {
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 (length(col) > 1) {
warning("argument 'col' has length > 1 and only the first element will be used")
col <- col[1]
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]
}
col <- as.character(col)
if (!is.data.frame(tbl)) {
stop("`tbl` must be a data.frame")
search_string <- as.character(search_string)
if (!is.data.frame(x)) {
stop("`x` must be a data.frame")
}
if (col %in% colnames(tbl)) {
ab_result <- col
if (search_string %in% colnames(x)) {
ab_result <- search_string
} else {
# sort colnames on length - longest first
cols <- colnames(tbl[, tbl %>% colnames() %>% nchar() %>% order() %>% rev()])
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$abs == as.ab(col)), "cols"]
ab_result <- df_trans[which(df_trans$abs == as.ab(search_string)), "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 `', col, '`.')
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 `", col, "`.")))
message(blue(paste0("NOTE: Using column `", bold(ab_result), "` as input for `", search_string, "`.")))
}
return(ab_result)
}