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unit tests

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dr. M.S. (Matthijs) Berends
2023-02-12 17:10:48 +01:00
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R/aa_options.R
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@ -29,7 +29,7 @@
#' Options for the AMR package
#'
#' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
#' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
#' @section Options:
#' * `AMR_custom_ab` \cr Allows to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
#' * `AMR_custom_mo` \cr Allows to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
@ -41,37 +41,37 @@
#' * `AMR_keep_synonyms` \cr A [logical] to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names.
#' * `AMR_locale` \cr A language to use for the `AMR` package, can be one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`.
#' * `AMR_mo_source` \cr A file location for a manual code list to be used in [as.mo()] and all [`mo_*`][mo_property()] functions. This is explained in [set_mo_source()].
#'
#'
#' @section Saving Settings Between Sessions:
#' Settings in \R are not saved globally and are thus lost when \R is exited. You can save your options to your own `.Rprofile` file, which is a user-specific file. You can edit it using:
#'
#'
#' ```r
#' utils::file.edit("~/.Rprofile")
#' ```
#'
#'
#' In this file, you can set options such as:
#'
#'
#' ```r
#' options(AMR_locale = "pt")
#' options(AMR_include_PKPD = TRUE)
#' ```
#'
#'
#' to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with [as.sir()].
#'
#'
#' ### Share Options Within Team
#'
#'
#' For a more global approach, e.g. within a data team, save an options file to a remote file location, such as a shared network drive. This would work in this way:
#'
#'
#' 1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
#'
#'
#' 2. For each user, open the `.Rprofile` file using `utils::file.edit("~/.Rprofile")` and put in there:
#'
#'
#' ```r
#' source("X:/team_folder/R_options.R")
#' ```
#'
#'
#' 3. Reload R/RStudio and check the settings with [getOption()], e.g. `getOption("AMR_locale")` if you have set that value.
#'
#'
#' Now the team settings are configured in only one place, and can be maintained there.
#' @keywords internal
#' @name AMR-options