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(v2.1.1.9078) 12 new formatting formats for antibiogram(), prepare for Bayesian WISCA

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dr. M.S. (Matthijs) Berends
2024-09-22 11:45:51 +02:00
parent 28bf91cbf5
commit 127892430d
8 changed files with 201 additions and 61 deletions
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R/aa_options.R
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@ -31,6 +31,7 @@
#'
#' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
#' @section Options:
#' * `AMR_antibiogram_formatting_type` \cr A [numeric] (1-12) to use in [antibiogram()], to indicate which formatting type to use.
#' * `AMR_breakpoint_type` \cr A [character] to use in [as.sir()], to indicate which breakpoint type to use. This must be either `r vector_or(clinical_breakpoints$type)`.
#' * `AMR_cleaning_regex` \cr A [regular expression][base::regex] (case-insensitive) to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to clean the user input. The default is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar".
#' * `AMR_custom_ab` \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].