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(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening

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dr. M.S. (Matthijs) Berends
2020-10-19 17:09:19 +02:00
parent 833a1be36d
commit 4e9ccb4435
76 changed files with 969 additions and 491 deletions
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18
R/guess_ab_col.R
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@ -30,7 +30,7 @@
#' @param x a [data.frame]
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a logical to indicate whether additional info should be printed
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precendence over shorter column names.**
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precedence over shorter column names.**
#' @return A column name of `x`, or `NULL` when no result is found.
#' @export
#' @inheritSection AMR Read more on our website!
@ -63,16 +63,13 @@
#' guess_ab_col(df, "ampicillin")
#' # [1] "AMP_ED20"
guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
meet_criteria(search_string, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(verbose, allow_class = "logical", has_length = 1)
if (is.null(x) & is.null(search_string)) {
return(as.name("guess_ab_col"))
}
stop_ifnot(is.data.frame(x), "`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
@ -116,6 +113,11 @@ get_column_abx <- function(x,
verbose = FALSE,
info = TRUE,
...) {
meet_criteria(x, allow_class = "data.frame")
meet_criteria(soft_dependencies, allow_class = "character", allow_NULL = TRUE)
meet_criteria(hard_dependencies, allow_class = "character", allow_NULL = TRUE)
meet_criteria(verbose, allow_class = "logical", has_length = 1)
meet_criteria(info, allow_class = "logical", has_length = 1)
if (info == TRUE) {
message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE)