Project creation with prodigenr: A component of reproducible and open scientific projects

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This R package is part of a series of (planned) packages that are aimed at creating a toolkit for doing reproducible and open science. Many researchers (especially in biomedicine, medicine, or health, which is my area of research) have little to no knowledge on what open science is or what reproducibility is, let alone how to do it. Our goal is create an (opinionated) toolkit to automate and simplify the process of doing open and reproducible science.

This package has a simple aim of being a project directory generator (prodigenr), with a simple focus on:

  1. Creating a standardized project folder structure with a few template files needed for beginning a data analysis project
  2. Following a “one project, one (main) output” principle, such as a report/manuscript in the case of scientific output or a book or website for things like courses or workshops
  3. Adhering to established best practices that make it easier for the project to be reproducible and open

This standardized approach to how a scientific project is structured helps ensure that the final code and documents are fairly modular, self-contained, easy to share and make public, and be as reproducible as possible. The structure also makes use of the existing and established applications and workflows (RStudio, devtools, and usethis).

Installation

You can install the released version of prodigenr from CRAN with:

install.packages("prodigenr")

And the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("rostools/prodigenr")

Usage

There are two ways of creating a new project: using the R console or using the RStudio “New Project” menu option.

Through the console, use the setup_project() command. So, for instance, if you want a manuscript project, type out:

library(prodigenr)
setup_project("~/Desktop/DiseaseDiet")

This then creates a directory tree, with template files for starting your analysis! Open the newly created project via the .Rproj file. For the RStudio approach, go to “File -> New Project”, then “New directory” and find the prodigenr project in the list:

Creating a prodigenr project in RStudio

Once in the project, you can add a manuscript R Markdown file using:

create_manuscript()

The main secondary function is the template_list command, which lists the available template files (submit a PR if you want another template included!):

template_list
#> [1] "report" "slides"

For a more detailed tutorial, see the introduction vignette:

vignette('prodigenr', 'prodigenr')

There are several existing packages for creating projects, each of which has it’s own pros and cons. Check out the last section of the vignette("prodigenr") for more details. Try them out and see which you like!

prodigenr tries to use ideas from R packages/devtools while still being as simple as possible and to be more specific to academic researchers primarily in biomedical/non-computer science fields. However, it can always improve! I welcome any suggestions, just submit a GitHub issue.

Interested in contributing?

See the contributing documentation for information on how to contribute. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Special thanks to @zsemnani for creating the logo!