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SCIproj

An R package for the initialization and organization of a scientific project following reproducible research and FAIR principles.

Overview

SCIproj is an R package that allows users to initialize a project through its function create_proj() and manage a scientific project as an R package or a research compendium. This combines structure, where files are located, and workflow, how analyses are reproduced or replicated.

The package is built on modern reproducibility standards and guidelines such as:

FAIR Principles - Findable, Accessible, Interoperable, Reusable research outputs
rOpenSci Reproducibility Guide - Best practices for reproducible research in R
TIER Protocol - Standards for transparent and reproducible data analysis
NASA TOPS - Open science and reproducibility guidelines

Defaults

The package has some default settings to ensure reproducibility. These include:

renv for dependency management: locks exact package versions for full reproducibility
targets for pipeline-based workflow: allows for automated dependency tracking, caching, and selective re-execution
CITATION.cff for machine-readable citation metadata (FAIR/open science)
DATA_SOURCES.md for documenting data provenance (source, license, DOI)
CONTRIBUTING.md for contribution guidelines
Git version control

Project structure

your-project/
├── DESCRIPTION             # Project metadata, dependencies, and author info (with ORCID).
├── README.Rmd              # Top-level project description.
├── your-project.Rproj      # RStudio project file.
├── CITATION.cff            # Machine-readable citation metadata for FAIR compliance.
├── CONTRIBUTING.md         # Contribution guidelines.
├── LICENSE.md              # Full license text (optional, requires add_license).
├── NAMESPACE               # Auto-generated by roxygen2 (do not edit by hand).
│
├── data-raw/               # Raw data files and pre-processing scripts.
│   ├── clean_data.R        # Script template for data cleaning.
│   ├── DATA_SOURCES.md     # Data provenance: source, license, DOI, download date.
│   └── ...
│
├── data/                   # Cleaned datasets stored as .rda files.
│
├── R/                      # Custom R functions and dataset documentation.
│   ├── function_ex.R       # Template for custom functions.
│   ├── data.R              # Template for dataset documentation.
│   └── ...
│
├── analyses/               # R scripts or R Markdown/Quarto documents for analyses.
│   ├── figures/            # Generated plots.
│   └── ...
│
├── docs/                   # Publication-ready documents (article, report, presentation).
├── trash/                  # Temporary files that can be safely deleted.
│
├── _targets.R              # Pipeline definition for reproducible workflow (default).
├── renv/                   # renv library and settings (default).
├── renv.lock               # Lockfile for reproducible package versions (default).
└── Dockerfile              # Container definition for full reproducibility (optional).

Why an R package as research compendium?

Separation of concerns: Raw data, clean data, functions, analyses, and manuscripts each live in dedicated folders.
Documented data: Clean datasets are stored as .rda files with roxygen documentation.
Reproducible workflow: The targets pipeline tracks dependencies automatically - only re-run what changed.
Locked dependencies: renv ensures the exact same package versions are used everywhere.
Citable and FAIR: CITATION.cff makes the project machine-readable and citable, DATA_SOURCES.md documents data provenance.
Load and go: devtools::load_all() instantly makes all clean datasets and custom functions available.

Installation and usage

Install the development version from GitHub:

### Using remotes
# install.packages("remotes")
remotes::install_github("saskiaotto/SCIproj")

### Or better: using the new pak package
# install.packages("pak")
pak::pkg_install("saskiaotto/SCIproj")

Creating the project

library("SCIproj")
create_proj("my_research_project")

This creates a project with renv, targets, CITATION.cff, and DATA_SOURCES.md by default.

Customize with parameters:

### Full-featured project with GitHub, CI, and ORCID
create_proj("my_research_project",
  add_license = "MIT",
  license_holder = "Jane Doe",
  orcid = "0000-0001-2345-67893",
  create_github_repo = TRUE,
  ci = "gh-actions"
)

### Minimal project without workflow tools
create_proj("my_research_project",
  use_renv = FALSE,
  use_targets = FALSE
)

Parameters

Parameter	Default	Description
`data_raw`	`TRUE`	Add `data-raw/` folder with templates
`makefile`	`FALSE`	Add `makefile.R` template
`testthat`	`FALSE`	Add testthat infrastructure
`use_pipe`	`FALSE`	Add magrittr pipe (native `\\|>` recommended)
`add_license`	`NULL`	License type: `"MIT"`, `"GPL"`, `"Apache"`, etc.
`license_holder`	`"Your name"`	License holder / project author
`orcid`	`NULL`	ORCID iD for CITATION.cff
`use_git`	`TRUE`	Initialize local git repo
`create_github_repo`	`FALSE`	Create GitHub repo (needs `GITHUB_PAT`)
`ci`	`"none"`	CI type: `"none"` or `"gh-actions"`
`use_renv`	`TRUE`	Initialize renv for dependency management
`use_targets`	`TRUE`	Add `_targets.R` pipeline template
`use_docker`	`FALSE`	Add Dockerfile template
`open_proj`	`FALSE`	Open new project in RStudio

Developing the project

Create the project with create_proj().
Edit DESCRIPTION with project metadata: title, summary, contributors (with ORCID), license, dependencies.
Edit README.Rmd with project details: objectives, timeline, workflow.
Document your data provenance in data-raw/DATA_SOURCES.md: source, license, download date, DOI for each dataset.
Place original (raw) data in data-raw/. Use clean_data.R (or more scripts) for pre-processing. Store clean datasets with usethis::use_data().
Document clean datasets using roxygen in R/ (see template data.R). For details, see Documenting data.
Place custom functions in R/ with roxygen documentation. See the documentation chapter in the R Packages book.
Write tests for your functions in tests/ (set testthat = TRUE in create_proj()). See Testing basics.
Place analysis scripts/notebooks in analyses/. Save plots in analyses/figures/.
Place final manuscripts, reports, and presentations in docs/. Use R Markdown, Quarto, or templates from rticles, thesisdown, or Quarto journal extensions.
Keep dependencies in sync: usethis::use_package() for DESCRIPTION, renv::snapshot() for the lockfile.
Update CITATION.cff when you archive your project or publish.

Workflow

Load the project: devtools::load_all() or Ctrl/Cmd + Shift + L in RStudio.
Build documentation: devtools::document() or Ctrl/Cmd + Shift + D.
Run tests: devtools::test() or Ctrl/Cmd + Shift + T.
Run the pipeline: targets::tar_make() to execute all targets. targets::tar_visnetwork() to visualize dependencies.
Update lockfile: renv::snapshot() after installing or updating packages.

For a detailed introduction to targets, see the user manual.

For maximum reproducibility, consider also using Docker (use_docker = TRUE). See the Rocker Project for R-specific Docker images.

Archiving and DOI

When your project is finalized:

Archive the GitHub repo to make it read-only.
Get a DOI via Zenodo (integrates directly with GitHub) or another DOI Registration Agency.
Update CITATION.cff with the DOI.
Optionally, generate a codemeta.json with codemetar::write_codemeta() for richer metadata.

Useful resources

Guidelines and standards

FAIR Principles - Findable, Accessible, Interoperable, Reusable
TIER Protocol - Teaching Integrity in Empirical Research
NASA TOPS Open Science - Transform to Open Science
The Turing Way - A guide to reproducible, ethical, and collaborative data science
The rOpenSci guide: Reproducibility in Science

R packages and tools

R Packages (2nd edition) by Hadley Wickham and Jenny Bryan
The targets R Package User Manual by Will Landau
renv: Project Environments

Research compendium concept

Gentleman, R. & Temple Lang, D. (2004): Statistical Analyses and Reproducible Research. Bioconductor Project Working Papers. Working Paper 2
Noble, W.S. (2009): A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. https://doi.org/10.1371/journal.pcbi.1000424
Marwick, B., Boettiger, C., & Mullen, L. (2018). Packaging data analytical work reproducibly using R (and friends). The American Statistician 72(1), 80-88. https://doi.org/10.1080/00031305.2017.1375986
Karthik Ram (2019): How To Make Your Data Analysis Notebooks More Reproducible. Presentation at the rstudio::conf(2019)

Credits

Francisco Rodriguez-Sanchez and his template package
Ben Marwick and his rrtools package
The group of participants in the Reproducible Science Curriculum Workshop that created the rr-init package

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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