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(v2.1.1.9081) HUGE microorganisms update for fungi!

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dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
parent a558f4c121
commit ac1c40d8bb
119 changed files with 36445 additions and 67400 deletions
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R/bug_drug_combinations.R
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@ -31,7 +31,7 @@
#'
#' 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 and I should be summed, so resistance will be based on only R - the default is `TRUE`
#' @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()]