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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
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R/bug_drug_combinations.R
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@ -31,13 +31,13 @@
#'
#' 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*.
#' @inheritParams eucast_rules
#' @param combine_SI a [logical] to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is `TRUE`
#' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
#' @param combine_SI A [logical] to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is `TRUE`
#' @param add_ab_group A [logical] to indicate where the group of the antimicrobials must be included as a first column
#' @param remove_intrinsic_resistant [logical] to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
#' @param FUN the function to call on the `mo` column to transform the microorganism codes - the default is [mo_shortname()]
#' @param translate_ab a [character] of length 1 containing column names of the [antimicrobials] data set
#' @param include_n_rows a [logical] to indicate if the total number of rows must be included in the output
#' @param ... arguments passed on to `FUN`
#' @param FUN The function to call on the `mo` column to transform the microorganism codes - the default is [mo_shortname()]
#' @param translate_ab A [character] of length 1 containing column names of the [antimicrobials] data set
#' @param include_n_rows A [logical] to indicate if the total number of rows must be included in the output
#' @param ... Arguments passed on to `FUN`
#' @inheritParams sir_df
#' @inheritParams base::formatC
#' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].