A template R workflow for general data analysis

This repository is a template for a docker-containerised, {targets}-based, {renv}-enabled R workflow for general data analysis.

About the Project

Repository Structure

The project repository is structured as follows:

sc-policy-review
    |-- .github/
    |-- data/
    |-- data-raw/
    |-- outputs/
    |-- R/
    |-- reports
    |-- renv
    |-- renv.lock
    |-- .Rprofile
    |-- packages.R
    |-- _targets.R

• .github contains project testing and automated deployment of outputs workflows via continuous integration and continuous deployment (CI/CD) using Github Actions.

• data/ contains intermediate and final data outputs produced by the workflow.

• data-raw/ contains raw datasets, usually either downloaded from source or added manually, that are used in the project.

• outputs/ contains compiled reports and figures produced by the workflow.

• R/ contains functions developed/created specifically for use in this workflow.

• reports/ contains literate code for R Markdown and/or Quarto reports rendered in the workflow.

• renv/ contains renv package specific files and directories used by the package for maintaining R package dependencies within the project. The directory renv/library, is a library that contains all packages currently used by the project. This directory, and all files and sub-directories within it, are all generated and managed by the renv package. Users should not change/edit these manually.

• renv.lock file is the renv lockfile which records enough metadata about every package used in this project that it can be re-installed on a new machine. This file is generated by the renv package and should not be changed/edited manually.

• .Rprofile file is a project R profile generated when initiating renv for the first time. This file is run automatically every time R is run within this project, and renv uses it to configure the R session to use the renv project library.

• packages.R file lists out all R package dependencies required by the workflow.

• _targets.R file defines the steps in the workflow’s data ingest, data processing, data analysis, and reporting pipeline.

Reproducibility

R package dependencies

This project was built using R 4.5.1. This project uses the renv framework to record R package dependencies and versions. Packages and versions used are recorded in renv.lock and code used to manage dependencies is in renv/ and other files in the root project directory. On starting an R session in the working directory, run renv::restore() to install R package dependencies.