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(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'

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dr. M.S. (Matthijs) Berends
2025-01-17 12:09:39 +01:00
parent 1697ad37ce
commit 92c4fc0f94
33 changed files with 1029 additions and 807 deletions
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R/antibiogram.R
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@ -31,7 +31,7 @@
#'
#' Create detailed antibiograms with options for traditional, combination, syndromic, and Bayesian WISCA methods. Based on the approaches of Klinker *et al.*, Barbieri *et al.*, and the Bayesian WISCA model (Weighted-Incidence Syndromic Combination Antibiogram) by Bielicki *et al.*, this function provides flexible output formats including plots and tables, ideal for integration with R Markdown and Quarto reports.
#' @param x a [data.frame] containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see [as.sir()])
#' @param antibiotics vector of any antibiotic name or code (will be evaluated with [as.ab()], column name of `x`, or (any combinations of) [antibiotic selectors][antibiotic_class_selectors] such as [aminoglycosides()] or [carbapenems()]. For combination antibiograms, this can also be set to values separated with `"+"`, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in `x`. See *Examples*.
#' @param antibiotics vector of any antibiotic name or code (will be evaluated with [as.ab()], column name of `x`, or (any combinations of) [antimicrobial selectors][antimicrobial_class_selectors] such as [aminoglycosides()] or [carbapenems()]. For combination antibiograms, this can also be set to values separated with `"+"`, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in `x`. See *Examples*.
#' @param mo_transform a character to transform microorganism input - must be `"name"`, `"shortname"` (default), `"gramstain"`, or one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
#' @param ab_transform a character to transform antibiotic input - must be one of the column names of the [antibiotics] data set (defaults to `"name"`): `r vector_or(colnames(antibiotics), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
#' @param syndromic_group a column name of `x`, or values calculated to split rows of `x`, e.g. by using [ifelse()] or [`case_when()`][dplyr::case_when()]. See *Examples*.