Generate folder structures for research compendiums

make_compendium generates the folder structure of a research compendium.

Usage

make_compendium(name = "research_compendium", path = ".", force = FALSE,
format = "basic", packrat = FALSE,
git = FALSE, clone = NULL, readme = TRUE, Rproj = FALSE)

Arguments

name: character string: the research compendium directory name. No special characters should be used. Default is "research_compendium".
path: Path to put the project directory in. Default is current directory.
force: Logical controlling whether existing folders with the same name are used for setting the folder structure. The function will never overwrite existing files or folders.
format: A character vector of length 1 with the name of the built-in compendiums available in the example object `compendiums` (see compendiums for available formats). Default is 'basic'. Alternatively, it can be a character vector with 2 or more elements with the names of the folders and subfolders to be included.
packrat: Logical to control if packrat is initialized (packrat::init()) when creating the compendium. Default is FALSE.
git: Logical to control if a git repository is initialized (git2r::init()) when creating the compendium. Default is FALSE.
clone: Path to a directory containing a folder structure to be cloned. Default is NULL. If provided 'format' is ignored. Folders starting with ^\.git|^\.Rproj.user|^\.\.Rcheck will be ignored.
readme: Logical. Controls if a readme file (in Rmd format) is added to the project. The file has predefined fields for documenting objectives and current status of the project. Default is TRUE.
Rproj: Logical. If TRUE a R project is created (i.e. a .Rproj file is saved in the main project directory).

Value

A folder skeleton for a research compendium. In addition the structure of the compendium is printed in the console. If the compendium format includes a "manuscript" or "doc(s)" folder the function saves a manuscript template in Rmarkdown format ("manuscript.Rmd"), a BibTex file ("example_library.bib", for showing how to add citations) and APA citation style file ("apa.csl") inside that folder.

Details

The function takes predefined folder structures to generate the directory skeleton of a research compendium.

References

Araya-Salas, M., Arriaga, A. (2023), sketchy: research compendiums for data analysis in R. R package version 1.0.3.Marwick, B., Boettiger, C., & Mullen, L. (2018). Packaging Data Analytical Work Reproducibly Using R (and Friends). American Statistician, 72(1), 80-88.Alston, J., & Rick, J. (2020). A Beginners Guide to Conducting Reproducible Research.

Author

Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)

Examples

{
data(compendiums)

make_compendium(name = "mycompendium", path = tempdir(), format = "basic",
force = TRUE)
}
#> Creating directories ...
#> mycompendium
#> │   
#> ├── data/  
#> │   ├── processed/  # modified/rearranged data
#> │   └── raw/  # original data
#> ├── manuscript/  # manuscript/poster figures
#> ├── output/  # all non-data products of data analysis
#> └── scripts/  # code
#> Done.
#>