Writing reprocible geoscience papers using R Markdown, Docker, and GitLab

This repository contains the course material for the EGU General Assembly 2018 short course "Writing reprocible geoscience papers using R Markdown, Docker, and GitLab". It is co-organised by Daniel Nüst, Vicky Steeves, Markus Konkol, and Edzer Pebesma.


This course website is based on the bookdown package, built automatically with the GitLab CI (see file .gitlab-ci.yml and work by Romain Lesur and available online in various formats: LINK HERE

You can build the page and all output formats locally with

bookdown::render_book("index.Rmd", "all", output_dir = "public")

Or just use the "Build" > "Build Book" - Button in RStudio.


Instructions partly based on A minimal book example using bookdown.

  • Each Rmd file contains one and only one chapter, and a chapter is defined by the first-level heading #.
  • Each sentence is on a seperate line to improve git merges and change tracking.
  • packages.bib includes a bib database for R packages; it can be created with the command below.
  .packages(), 'bookdown', 'knitr', 'rmarkdown', 'rticles'
), 'packages.bib')
  • Write citations for packages, e.g. [@R-bookdown] and papers, e.g. [@xie2015].
  • Label chapters and sections using {#label} in the headlines and reference as \@ref(label).

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