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Add add_if_missing parameter to control NA handling in interpretive rules (#264)

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Matthijs Berends
2026-04-21 21:53:43 +02:00
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parent fb8758f36b
commit 8ff5d4472a
46 changed files with 1232 additions and 1016 deletions
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R/antibiogram.R
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@@ -48,8 +48,8 @@
#' - `carbapenems() + "GEN"`
#' - `carbapenems() + c("", "GEN")`
#' - `carbapenems() + c("", aminoglycosides())`
#' @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 or `NA` to consider all microorganisms 'unknown'.
#' @param ab_transform A character to transform antimicrobial input - must be one of the column names of the [antimicrobials] data set (defaults to `"name"`): `r vector_or(colnames(antimicrobials), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
#' @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, documentation = TRUE)`. Can also be `NULL` to not transform the input or `NA` to consider all microorganisms 'unknown'.
#' @param ab_transform A character to transform antimicrobial input - must be one of the column names of the [antimicrobials] data set (defaults to `"name"`): `r vector_or(colnames(antimicrobials), sort = FALSE, documentation = 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*.
#' @param add_total_n *(deprecated in favour of `formatting_type`)* A [logical] to indicate whether `n_tested` available numbers per pathogen should be added to the table (default is `TRUE`). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for *E. coli* 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when `wisca = TRUE`; in that case, use [retrieve_wisca_parameters()] to get the parameters used for WISCA.
#' @param only_all_tested (for combination antibiograms): a [logical] to indicate that isolates must be tested for all antimicrobials, see *Details*.