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Create a package or research compendium structure

Source: R/rcompendium-package.R
rcompendium-package.Rd

rcompendium makes easier the creation of R packages or research compendia (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with 'testthat', and build and deploy website using 'pkgdown').

  1. Store your credentials (given and family names, email, ORCID, etc.) with set_credentials() (if not already done);

  2. Create an new empty RStudio project;

  3. Run new_package() to create a new package structure or new_compendium() to create a new research compendium structure;

  4. Edit some metadata in DESCRIPTION, CITATION, and README.Rmd;

  5. Start working (add data, write and document R functions, etc.);

  6. And do not forget to commit your changes.

Managing credentials

You can use the arguments given, family, email, and orcid directly with the functions new_*() and add_*(). But if you create a lot a projects (packages and/or compendia) it can be frustrating in the long run.

An alternative way is to use ONCE AND FOR ALL the function set_credentials() to permanently store this information in the ~/.Rprofile file. If these arguments are set to NULL while calling any function of the package, rcompendium will search their values in this file. It will save your time (it's the purpose of this package).

Even if you have stored your credentials in the ~/.Rprofile file you will always be able to modify them on-the-fly (i.e. by using credentials arguments in the functions new_*() and add_*()) or permanently by re-running set_credentials().

Configuring git

To see if git is correctly configured on your laptop, run gh::gh_whoami(). You should see something like:

{
  "name": "John Doe",
  "login": "jdoe",
  "html_url": "https://github.com/jdoe",
  ...
}

Otherwise you might need to run:

gert::git_config_global_set(name  = "user.name", 
                            value = "John Doe")
                            
gert::git_config_global_set(name  = "user.email", 
                            value = "john.doe@domain.com")
                            
gert::git_config_global_set(name  = "github.user", 
                            value = "jdoe")

See gert::git_config_global_set() for further information.

Creating a GitHub repo

To create the GitHub repository directly from R, the package rcompendium uses the function usethis::use_github(), a client to the GitHub REST API. The interaction with this API required an authentication method: a GITHUB PAT (Personal Access Token).

If you don't have a GITHUB PAT locally stored, you must:

  1. Visit the page https://github.com/settings/tokens and create a new token;

  2. Store it in the ~/.Renviron file by using usethis::edit_r_environ() and adding the following line: GITHUB_PAT='ghp_99z9...z9'.

Run usethis::gh_token_help() for more information about getting and configuring a GITHUB PAT.

If everything is well configured, you should see something like this after calling gh::gh_whoami():

{
  "name": "John Doe",
  "login": "jdoe",
  "html_url": "https://github.com/jdoe",
  "scopes": "repo, workflow",
  "token": "ghp_...z99Z"
}

Resources

See also

Useful links:

Author

Maintainer: Nicolas Casajus nicolas.casajus@fondationbiodiversite.fr (ORCID) [copyright holder]