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(v2.1.1.9232) is.mic() iteration, documentation cleanup

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dr. M.S. (Matthijs) Berends
2025-03-31 10:51:31 +02:00
parent 5f5b77bfaf
commit 63099cd81e
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R/key_antimicrobials.R
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@@ -30,15 +30,15 @@
#' (Key) Antimicrobials for First Weighted Isolates
#'
#' These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see [first_isolate()]). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.
#' @param x a [data.frame] with antimicrobials columns, like `AMX` or `amox`. Can be left blank to determine automatically.
#' @param x A [data.frame] with antimicrobials columns, like `AMX` or `amox`. Can be left blank to determine automatically.
#' @param y,z [character] vectors to compare
#' @inheritParams first_isolate
#' @param universal names of **broad-spectrum** antimicrobial drugs, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antimicrobial drugs
#' @param gram_negative names of antibiotic drugs for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs
#' @param gram_positive names of antibiotic drugs for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs
#' @param antifungal names of antifungal drugs for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antifungal drugs
#' @param only_sir_columns a [logical] to indicate whether only columns must be included that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`)
#' @param ... ignored, only in place to allow future extensions
#' @param universal Names of **broad-spectrum** antimicrobial drugs, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antimicrobial drugs
#' @param gram_negative Names of antibiotic drugs for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs
#' @param gram_positive Names of antibiotic drugs for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs
#' @param antifungal Names of antifungal drugs for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antifungal drugs
#' @param only_sir_columns A [logical] to indicate whether only columns must be included that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`)
#' @param ... Ignored, only in place to allow future extensions
#' @details
#' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#'