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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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R/guess_ab_col.R
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@ -29,12 +29,12 @@
#' Guess Antibiotic Column
#'
#' This tries to find a column name in a data set based on information from the [antibiotics] data set. Also supports WHONET abbreviations.
#' This tries to find a column name in a data set based on information from the [antimicrobials] data set. Also supports WHONET abbreviations.
#' @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
#' @param only_sir_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`)
#' @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.
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antimicrobials] data set for any column containing a name or code of that antibiotic.
#' @return A column name of `x`, or `NULL` when no result is found.
#' @export
#' @examples