My looseleaf: Overview

looseleaf :leaves:

Research compendium template for tracking, linking, and sharing data explorations

Motivation

It is difficult to manage a linked collection of R notebooks.

bookdown is great except for a few key downsides arising from the fact that chapters are concatenated on render so that chunk labels cannot be duplicated, selective caching becomes difficult, and there can be no chapter level knitr hooks.

Features

• rmarkdown files are only re-built if they have changed since the last rebuild

• turn off chapter/page evaluation (or message printing) with a single knitr hook

• a looseleaf build will continue despite evaluation errors

• keep track of R package dependencies in DESCRIPTION

Example

https://jsta.github.io/looseleaf

Usage

• Clone this repo

• Do not edit the auto-generated files in _site

Workflow

1. Create an Rmd file with the yaml header and chunk options in the provided template

2. Add CRAN and Github package dependencies to DESCRIPTION

3. Call make looseleaf-md from the command line (see required R packages for all projects in setup.md)

4. Render to html (3 options)

   • locally using make serve (see optional system dependencies in setup.md)

   • remotely for public repos by enabling Github pages

   • remotely for private repos by building a zip file on Gitlab CI (see .gitlab-ci.yml)

Prior art

https://github.com/swcarpentry/styles