Create an R compendium structure

This function creates a research compendium (i.e. a predefined files/folders structure) to help user organizing files/folders to run analysis.

In addition to common R packages files/folders (see new_package() for further information) this function will created these following folders:

data/: a folder to store raw data. Note that these data must never be modified. If user want to modify them it is recommended to export new data in outputs/.
analyses/: a folder to write analyses instructions, i.e. R scripts. If user need to create R functions it is recommended to write them in the R/ folder.
outputs/: a folder to store intermediate and final outputs generated by the R scripts.
figures/: a folder to store figures generated by the R scripts.

This function also creates a Make-like R file (make.R). This file contains two main lines:

devtools::install_deps(): downloads the external dependencies required by the project (an alternative to install.packages()). Ideal for sharing;
devtools::load_all(): loads external dependencies and R functions (an alternative to library() and source() respectively).

As the user writes R scripts he/she can add the following line in this file: source(here::here("rscripts", "script_X.R")). Then he/she can source the entire make.R to run analysis. The function add_dependencies() can be used to automatically add external dependencies in the DESCRIPTION file.

It is recommended, for a better reproducibility, to call external dependencies as pkg::fun() or with @import or @importFrom in R functions instead of using library().

All these files/folders are added to the .Rbuildignore so the rest of the project (e.g. R functions) can be used (or installed) as a R package.

Usage

new_compendium(
  compendium = NULL,
  license = "GPL (>= 2)",
  status = NULL,
  lifecycle = NULL,
  contributing = TRUE,
  code_of_conduct = TRUE,
  vignette = FALSE,
  test = FALSE,
  create_repo = TRUE,
  private = FALSE,
  gh_check = FALSE,
  codecov = FALSE,
  website = FALSE,
  gh_render = FALSE,
  gh_citation = FALSE,
  given = NULL,
  family = NULL,
  email = NULL,
  orcid = NULL,
  organisation = NULL,
  renv = FALSE,
  dockerfile = FALSE,
  overwrite = FALSE,
  quiet = FALSE
)

Arguments

compendium

A character vector specifying the folders to be created. See add_compendium() for further information.

license

A character vector of length 1. The license to be used for this project. Run get_licenses() to choose an appropriate one. Default is license = 'GPL (>= 2)'

The license can be changed later by calling add_license() (and add_license_badge() or refresh() to update the corresponding badge in the README).

status

A character vector of length 1. The status of the project according to the standard defined by the https://www.repostatus.org project. One among 'concept', 'wip', 'suspended', 'abandoned', 'active', 'inactive', or 'unsupported'. See add_repostatus_badge() for further information.

This argument is used to add a badge to the README.Rmd to help visitors to better understand your project. Default is status = NULL.

This status can be added/changed later by using add_repostatus_badge().

lifecycle

A character vector of length 1. The life cycle stage of the project according to the standard defined at https://lifecycle.r-lib.org/articles/stages.html. One among 'experimental', 'stable', 'deprecated', or 'superseded'. See add_lifecycle_badge() for further information.

This argument is used to add a badge to the README.Rmd to help visitors to better understand your project. Default is lifecycle = NULL.

This stage can be added/changed later by using add_lifecycle_badge().

contributing

A logical value. If TRUE (default) adds a CONTRIBUTING.md file and ISSUE_TEMPLATES. See add_contributing() for further information.

code_of_conduct

A logical value. If TRUE (default) adds a CODE_OF_CONDUCT.md file. See add_code_of_conduct() for further information.

vignette

A logical value. If TRUE creates a vignette in vignettes/. Packages knitr and rmarkdown are also added to the Suggests field in the DESCRIPTION file. Default is FALSE.

test

A logical value. If TRUE initializes units tests by running usethis::use_testthat(). Package testthat is also added to the Suggests field in the DESCRIPTION file. Default is FALSE.

create_repo

A logical value. If TRUE (default) creates a repository (public if private = FALSE or private if private = TRUE) on GitHub. See the section Creating a GitHub repo of the help page of new_package().

private

A logical value. If TRUE creates a private repository on user GitHub account (or organisation). Default is private = FALSE.

gh_check

A logical value. If TRUE configures GitHub Actions to automatically check and test the package after each push. This will run R CMD check on the three major operating systems (Ubuntu, macOS, and Windows) on the latest release of R. See add_github_actions_check() for further information.