Options for the AMR packageSource:
This is an overview of all the package-specific
options() you can set in the
Allows to use custom antimicrobial drugs with this package. This is explained in
Allows to use custom microorganisms with this package. This is explained in
Used for setting the default types of rules for
eucast_rules()function, must be one or more of:
"all", and defaults to
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 to the latest implemented EUCAST guideline, currently
"EUCAST 2023". Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).
A logical to use in
mo_*functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is
A regular expression (case-insensitive) to use in
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".
A language to use for the
AMRpackage, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported).
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:
In this file, you can set options such as:
to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with
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:
Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
For each user, open the
utils::file.edit("~/.Rprofile")and put in there:
Reload R/RStudio and check the settings with
getOption("AMR_locale")if you have set that value.
Now the team settings are configured in only one place, and can be maintained there.