AMR-options {AMR}R Documentation

Options for the AMR package

Description

This is an overview of all the package-specific options() you can set in the AMR package.

Options

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 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:

  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.


[Package AMR version 3.0.0 Index]