Writing Reproducible Research Papers with R Markdown

This repository holds the materials for a workshop on writing reproducible research papers with R Markdown, first taught at Campus Luzern in March 2020.

Unless otherwise noted, all material is copyright Resul Umit, licensed CC-BY-SA 3.0. An easy to read summary of this permissive licence is available on the Creative Commons website.

Contents

The workshop is divided into ten parts. Most parts include exercises — 40+ in total.

Material

Below are the workshop materials kept in this repository.

• manuscript\reproduce_this.pdf

  • a document, formatted in Word but saved as PDF, to be re-created with R Markdown
  • random sentences in the document are generated with the stringi package (Gagolewski, 2020)
  • figures and tables are based on a fabricated dataset (journals.csv, see below)
  • key sections in-need of attention are highlighted

• manuscript\journals.Rmd

  • an R Markdown document to work on during the workshop
    • includes unformatted text from reproduce_this.pdf to save time
    • major components, such as paragraphs and tables, are numbered and marked in comments to facilitate navigation

• manuscript\references.bib

  • a BibTeX document with three fabricated references

• manuscript\apa_7th.csl

  • a Citation Style Language document, with APA (7th Edition) referencing style (Wiernik, 2020)

• data\journals.csv

  • a dataset created with the fabricatr package (Blair et al., 2019), imagined to explore the Google Scholar rankings of fictitious journals

  • includes the following variables

    • name: journals (1090 random titles)
    • origin: geographic origins (five continents)
    • branch: major discipline of journals (four branches)
    • since: time of first publication (years)
    • h5_index: H5 Index (integers)
    • h5_median: H5 Median (integers)
    • english: English (1) vs. other-language (0) journals
    • subfield: subfield (1) vs. generalist (0) journals
    • issues: number of issues published per year (integers)

• image\google_scholar.png

  • a screeenshot image of the Google Scholar homapage, copyright Google, LLC

• presentation\rmd_workshop.pdf

  • slides in PDF format
  • HTML version is available at https://resulumit.com/teaching/rmd_workshop.html
    • offers, among others, the ability to scroll across long codes on some slides

• presentation\rmd_workshop.Rmd

  • an R Markdown file behind the slides, produced with the xaringan package (Xie, 2020)

• test\run_this.R

  • an R script that
    • installs the packages needed for the workshop
    • attempts to knit an R Markdown into PDF file
  • useful for tasking participants with a pre-workshop setup

• test\the_test.Rmd

  • an R Markdown file, to be used for the attempt in test\run_this.R

References

Blair, G., Cooper, J., Coppock, A., Humphreys, M., Rudkin, A. and Fultz, N. (2019). fabricatr: Imagine your data before you collect it. R package, version 0.10.0.

Gagolewski, M. (2020). stringi: Character String Processing Facilities. R package, version 1.4.6.

Wiernik, B. M. (2020). American Psychological Association 7th edition (no ampersand). Citation style language file, version 1.0.

Xie, Y. (2020). xaringan: Presentation Ninja. R package, version 0.18.