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

(v2.1.1.9232) is.mic() iteration, documentation cleanup

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-31 10:51:31 +02:00
parent 5f5b77bfaf
commit 63099cd81e
93 changed files with 1001 additions and 990 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
R/random.R
View File

@ -30,11 +30,11 @@
#' Random MIC Values/Disk Zones/SIR Generation
#'
#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
#' @param size desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank.
#' @param mo any [character] that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any [character] that can be coerced to a valid antimicrobial drug code with [as.ab()]
#' @param prob_SIR a vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value)
#' @param ... ignored, only in place to allow future extensions
#' @param size Desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank.
#' @param mo Any [character] that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab Any [character] that can be coerced to a valid antimicrobial drug code with [as.ab()]
#' @param prob_SIR A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value)
#' @param ... Ignored, only in place to allow future extensions
#' @details The base \R function [sample()] is used for generating values.
#'
#' Generated values are based on the EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` guideline as implemented in the [clinical_breakpoints] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.