P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-21 10:53:18 +02:00
Code Releases Activity

(v2.1.1.9233) chore: make all argument texts full sentences

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-31 14:53:24 +02:00
parent 63099cd81e
commit 1fdab84103
91 changed files with 720 additions and 701 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
R/mic.R
View File

@ -60,10 +60,10 @@ COMMON_MIC_VALUES <- c(
#'
#' This transforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
#' @rdname as.mic
#' @param x A [character] or [numeric] vector
#' @param na.rm A [logical] indicating whether missing values should be removed
#' @param x A [character] or [numeric] vector.
#' @param na.rm A [logical] indicating whether missing values should be removed.
#' @param keep_operators A [character] specifying how to handle operators (such as `>` and `<=`) in the input. Accepts one of three values: `"all"` (or `TRUE`) to keep all operators, `"none"` (or `FALSE`) to remove all operators, or `"edges"` to keep operators only at both ends of the range.
#' @param ... Arguments passed on to methods
#' @param ... Arguments passed on to methods.
#' @details To interpret MIC values as SIR values, use [as.sir()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
#'
#' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers: