P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 04:02:19 +02:00
Code Releases Activity

(v1.6.0.9021) join functions update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
R/bug_drug_combinations.R
View File

@ -28,11 +28,11 @@
#' 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 publicable/printable format, see *Examples*.
#' @inheritSection lifecycle Stable Lifecycle
#' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group 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 function to call on the `mo` column to transform the microorganism IDs, defaults to [mo_shortname()]
#' @param translate_ab character of length 1 containing column names of the [antibiotics] data set
#' @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
#' @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 IDs, defaults to [mo_shortname()]
#' @param translate_ab a [character] of length 1 containing column names of the [antibiotics] data set
#' @param ... arguments passed on to `FUN`
#' @inheritParams rsi_df
#' @inheritParams base::formatC