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R
aa_amr-package.R
aa_globals.R
aa_helper_functions.R
aa_helper_pm_functions.R
aa_options.R
ab.R
ab_from_text.R
ab_property.R
age.R
amr_selectors.R
antibiogram.R
atc_online.R
av.R
av_from_text.R
av_property.R
availability.R
bug_drug_combinations.R
count.R
custom_antimicrobials.R
custom_eucast_rules.R
custom_mdro_guideline.R
custom_microorganisms.R
data.R
disk.R
eucast_rules.R
export_biosample.R
first_isolate.R
g.test.R
get_episode.R
ggplot_pca.R
ggplot_sir.R
guess_ab_col.R
italicise_taxonomy.R
join_microorganisms.R
key_antimicrobials.R
kurtosis.R
like.R
mdro.R
mean_amr_distance.R
mic.R
mo.R
mo_matching_score.R
mo_property.R
mo_source.R
pca.R
plotting.R
proportion.R
random.R
resistance_predict.R
sir.R
sir_calc.R
sir_df.R
skewness.R
sysdata.rda
top_n_microorganisms.R
translate.R
vctrs.R
whocc.R
zz_deprecated.R
zzz.R
data
data-raw
inst
man
pkgdown
tests
vignettes
.Rbuildignore
.gitignore
AMR.Rproj
CRAN-SUBMISSION
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
README.Rmd
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
index.Rmd
index.md
logo.svg
84 lines
7.1 KiB
R
Executable File
84 lines
7.1 KiB
R
Executable File
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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#' Options for the AMR package
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#'
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#' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
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#' @section Options:
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#' * `AMR_antibiogram_formatting_type` \cr A [numeric] (1-22) to use in [antibiogram()], to indicate which formatting type to use.
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#' * `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$type)`.
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#' * `AMR_capped_mic_handling` \cr A [character] to use in [as.sir()], to indicate how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. Must be one of `"standard"`, `"strict"`, `"relaxed"`, or `"inverse"` - the default is `"standard"`.
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#' * `AMR_cleaning_regex` \cr A [regular expression][base::regex] (case-insensitive) to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to clean the user input. The default is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar".
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#' * `AMR_custom_ab` \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
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#' * `AMR_custom_mo` \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
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#' * `AMR_eucastrules` \cr A [character] to set the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
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#' * `AMR_guideline` \cr A [character] to set the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default to the latest implemented EUCAST guideline, currently \code{"`r clinical_breakpoints$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)))`).
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#' * `AMR_ignore_pattern` \cr A [regular expression][base::regex] to ignore (i.e., make `NA`) any match given in [as.mo()] and all [`mo_*`][mo_property()] functions.
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#' * `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 - the default is `TRUE`.
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#' * `AMR_substitute_missing_r_breakpoint` \cr A [logical] to use in [as.sir()], to indicate that missing R breakpoints must be substituted with `"R"` - the default is `FALSE`.
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#' * `AMR_include_screening` \cr A [logical] to use in [as.sir()], to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`.
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#' * `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. The default is `FALSE`.
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#' * `AMR_locale` \cr A [character] to set the language for the `AMR` package, can be one of these supported language names or [ISO 639-1 codes](https://en.wikipedia.org/wiki/ISO_639-1): `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. The default is the current system language (if supported, English otherwise).
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#' * `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()].
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#'
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#' @section Saving Settings Between Sessions:
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#' 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:
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#'
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#' ```r
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#' utils::file.edit("~/.Rprofile")
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#' ```
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#'
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#' In this file, you can set options such as...
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#'
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#' ```r
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#' options(AMR_locale = "pt")
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#' options(AMR_include_PKPD = TRUE)
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#' ```
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#'
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#' ...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with [as.sir()].
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#'
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#' ### Share Options Within Team
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#'
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#' 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, and have each user read in this file automatically at start-up. This would work in this way:
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#'
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#' 1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
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#'
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#' 2. For each user, open the `.Rprofile` file using `utils::file.edit("~/.Rprofile")` and put in there:
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#'
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#' ```r
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#' source("X:/team_folder/R_options.R")
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#' ```
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#'
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#' 3. Reload R/RStudio and check the settings with [getOption()], e.g. `getOption("AMR_locale")` if you have set that value.
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#'
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#' Now the team settings are configured in only one place, and can be maintained there.
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#' @keywords internal
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#' @name AMR-options
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NULL
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