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add include_screening to as.sir()

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dr. M.S. (Matthijs) Berends
2023-02-12 15:09:54 +01:00
parent c740967cf2
commit 68abb00c59
9 changed files with 101 additions and 32 deletions
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10
R/aa_options.R
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@ -37,6 +37,7 @@
#' * `AMR_guideline` \cr Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default is \code{"`r clinical_breakpoints$guideline[1]`"}. Supported guideline are currently EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
#' * `AMR_ignore_pattern` \cr A [regular expression][base::regex] to define input that must be ignored in [as.mo()] and all [`mo_*`][mo_property()] functions.
#' * `AMR_include_PKPD` \cr A [logical] to use in [as.sir()], to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to `TRUE`.
#' * `AMR_include_screening` \cr A [logical] to use in [as.sir()], to indicate that clinical breakpoints for screening are allowed, defaults to `FALSE`.
#' * `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()].
@ -48,7 +49,14 @@
#' utils::file.edit("~/.Rprofile")
#' ```
#'
#' In this file, you can set options such as `options(AMR_locale = "pt")` for Portuguese language support of antibiotics.
#' 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
#'