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# Options for the AMR package

Source: `R/aa_options.R`
`AMR-options.Rd`

This is an overview of all the package-specific options you can set in the `AMR` package. Set them using the `options()` function, e.g.:

`options(AMR_guideline = "CLSI")`

## Options (alphabetical order)

- `AMR_antibiogram_formatting_type`
  A numeric (1-22) to use in `antibiogram()`, to indicate which formatting type to use.

- `AMR_breakpoint_type`
  A character to use in `as.sir()`, to indicate which breakpoint type to use. This must be either `"ECOFF"`, `"animal"`, or `"human"`.

- `AMR_capped_mic_handling`
  A character to use in `as.sir()`, to indicate how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. Must be one of `"none"`, `"conservative"`, `"standard"`, or `"lenient"` - the default is `"conservative"`.

- `AMR_cleaning_regex`
  A regular expression (case-insensitive) to use in `as.mo()` and all `mo_*` 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`
  A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in `add_custom_antimicrobials()`.

- `AMR_custom_mo`
  A file location to an RDS file, to use custom microorganisms with this package. This is explained in `add_custom_microorganisms()`.

- `AMR_eucastrules`
  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")`.

- `AMR_guideline`
  A character to set the default guideline used throughout the `AMR` package wherever a `guideline` argument is available. This option is used as the default in e.g. `as.sir()`, `resistance()`, `susceptibility()`, `interpretive_rules()` and many plotting functions. While unset, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2026).

  - For `as.sir()`, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST 2011 to 2026, and CLSI 2011 to 2026.

  - For `resistance()` and `susceptibility()`, this setting determines how the `"I"` (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, `"I"` is considered resistant in susceptibility calculations; under EUCAST, `"I"` is considered susceptible in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.

  - For `interpretive_rules()`, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.

  - For many plotting functions (e.g., for MIC or disk diffusion values), supplying `mo` and `ab` enables automatic SIR-based interpretative colouring. These colours are derived from `as.sir()` in the background and therefore depend on the active `guideline` setting, which again uses EUCAST 2026 if not set explicitly.

- `AMR_guideline`
  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 `"EUCAST 2026"`. Supported guideline are currently EUCAST (2011-2026) and CLSI (2011-2026).

- `AMR_ignore_pattern`
  A regular expression to ignore (i.e., make `NA`) any match given in `as.mo()` and all `mo_*` functions.

- `AMR_include_PKPD`
  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`.

- `AMR_substitute_missing_r_breakpoint`
  A logical to use in `as.sir()`, to indicate that missing R breakpoints must be substituted with `"R"` - the default is `FALSE`.

- `AMR_include_screening`
  A logical to use in `as.sir()`, to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`.

- `AMR_keep_synonyms`
  A logical to use in `as.mo()` and all `mo_*` functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`.

- `AMR_locale`
  A character to set the language for the `AMR` package, can be one of these supported language names or ISO 639-1 codes: English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Korean (ko), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr), Ukrainian (uk), Urdu (ur), or Vietnamese (vi). The default is the current system language (if supported, English otherwise).

- `AMR_mo_source`
  A file location for a manual code list to be used in `as.mo()` and all `mo_*` functions. This is explained in `set_mo_source()`.

## 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:

      utils::file.edit("~/.Rprofile")

In this file, you can set options such as...

     options(AMR_locale = "pt")
     options(AMR_include_PKPD = TRUE)

...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with `as.sir()`.

### Share Options Within Team

For a more collaborative 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:

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:

         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.