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dr. M.S. (Matthijs) Berends
2022-08-21 16:37:20 +02:00
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R/bug_drug_combinations.R
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@ -26,7 +26,6 @@
#' Determine Bug-Drug Combinations
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
#' @inheritSection lifecycle Stable Lifecycle
#' @inheritParams eucast_rules
#' @param combine_IR a [logical] to indicate whether values R and I should be summed
#' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
@ -41,11 +40,10 @@
#' @rdname bug_drug_combinations
#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "I", "R" and "total".
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' \donttest{
#' x <- bug_drug_combinations(example_isolates)
#' x
#' head(x)
#' format(x, translate_ab = "name (atc)")
#'
#' # Use FUN to change to transformation of microorganism codes