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reference/AMR-options.md
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reference/AMR-options.md
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# Options for the AMR package
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This is an overview of all the package-specific
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[`options()`](https://rdrr.io/r/base/options.html) you can set in the
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`AMR` package.
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## Options
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- `AMR_antibiogram_formatting_type`
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A [numeric](https://rdrr.io/r/base/numeric.html) (1-22) to use in
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[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md), to
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indicate which formatting type to use.
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- `AMR_breakpoint_type`
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A [character](https://rdrr.io/r/base/character.html) to use in
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
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which breakpoint type to use. This must be either "ECOFF", "animal",
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or "human".
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- `AMR_capped_mic_handling`
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A [character](https://rdrr.io/r/base/character.html) to use in
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
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how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted.
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Must be one of `"standard"`, `"strict"`, `"relaxed"`, or `"inverse"` -
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the default is `"standard"`.
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- `AMR_cleaning_regex`
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A [regular expression](https://rdrr.io/r/base/regex.html)
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(case-insensitive) to use in
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and all
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[`mo_*`](https://amr-for-r.org/reference/mo_property.md) functions, to
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clean the user input. The default is the outcome of
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[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md),
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which removes texts between brackets and texts such as "species" and
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"serovar".
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- `AMR_custom_ab`
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A file location to an RDS file, to use custom antimicrobial drugs with
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this package. This is explained in
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[`add_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md).
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- `AMR_custom_mo`
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A file location to an RDS file, to use custom microorganisms with this
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package. This is explained in
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[`add_custom_microorganisms()`](https://amr-for-r.org/reference/add_custom_microorganisms.md).
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- `AMR_eucastrules`
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A [character](https://rdrr.io/r/base/character.html) to set the
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default types of rules for
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[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
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function, must be one or more of: `"breakpoints"`, `"expert"`,
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`"other"`, `"custom"`, `"all"`, and defaults to
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`c("breakpoints", "expert")`.
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- `AMR_guideline`
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A [character](https://rdrr.io/r/base/character.html) to set the
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default guideline for interpreting MIC values and disk diffusion
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diameters with
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md). Can be only
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the guideline name (e.g., `"CLSI"`) or the name with a year (e.g.
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`"CLSI 2019"`). The default to the latest implemented EUCAST
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guideline, currently `"EUCAST 2025"`. Supported guideline are
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currently EUCAST (2011-2025) and CLSI (2011-2025).
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- `AMR_ignore_pattern`
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A [regular expression](https://rdrr.io/r/base/regex.html) to ignore
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(i.e., make `NA`) any match given in
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and all
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[`mo_*`](https://amr-for-r.org/reference/mo_property.md) functions.
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- `AMR_include_PKPD`
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A [logical](https://rdrr.io/r/base/logical.html) to use in
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
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that PK/PD clinical breakpoints must be applied as a last resort - the
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default is `TRUE`.
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- `AMR_substitute_missing_r_breakpoint`
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A [logical](https://rdrr.io/r/base/logical.html) to use in
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
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that missing R breakpoints must be substituted with `"R"` - the
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default is `FALSE`.
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- `AMR_include_screening`
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A [logical](https://rdrr.io/r/base/logical.html) to use in
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md), to indicate
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that clinical breakpoints for screening are allowed - the default is
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`FALSE`.
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- `AMR_keep_synonyms`
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A [logical](https://rdrr.io/r/base/logical.html) to use in
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and all
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[`mo_*`](https://amr-for-r.org/reference/mo_property.md) functions, to
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indicate if old, previously valid taxonomic names must be preserved
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and not be corrected to currently accepted names. The default is
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`FALSE`.
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- `AMR_locale`
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A [character](https://rdrr.io/r/base/character.html) to set the
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language for the `AMR` package, can be one of these supported language
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names or [ISO 639-1 codes](https://en.wikipedia.org/wiki/ISO_639-1):
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English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs),
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Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek
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(el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Korean
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(ko), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro),
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Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr),
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Ukrainian (uk), Urdu (ur), or Vietnamese (vi). The default is the
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current system language (if supported, English otherwise).
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- `AMR_mo_source`
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A file location for a manual code list to be used in
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and all
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[`mo_*`](https://amr-for-r.org/reference/mo_property.md) functions.
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This is explained in
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[`set_mo_source()`](https://amr-for-r.org/reference/mo_source.md).
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## Saving Settings Between Sessions
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Settings in R are not saved globally and are thus lost when R is exited.
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You can save your options to your own `.Rprofile` file, which is a
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user-specific file. You can edit it using:
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utils::file.edit("~/.Rprofile")
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In this file, you can set options such as...
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options(AMR_locale = "pt")
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options(AMR_include_PKPD = TRUE)
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...to add Portuguese language support of antimicrobials, and allow PK/PD
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rules when interpreting MIC values with
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md).
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### Share Options Within Team
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For a more global approach, e.g. within a (data) team, save an options
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file to a remote file location, such as a shared network drive, and have
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each user read in this file automatically at start-up. This would work
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in this way:
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1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill
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it with preferred settings.
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2. For each user, open the `.Rprofile` file using
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`utils::file.edit("~/.Rprofile")` and put in there:
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source("X:/team_folder/R_options.R")
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3. Reload R/RStudio and check the settings with
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[`getOption()`](https://rdrr.io/r/base/options.html), e.g.
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`getOption("AMR_locale")` if you have set that value.
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Now the team settings are configured in only one place, and can be
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maintained there.
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