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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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R/aa_options.R
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@ -31,7 +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_antibiogram_formatting_type` \cr A [numeric] (1-22) 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()].
@ -59,7 +59,7 @@
#' options(AMR_include_PKPD = TRUE)
#' ```
#'
#' ...to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with [as.sir()].
#' ...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with [as.sir()].
#'
#' ### Share Options Within Team
#'