This lesson is in the early stages of development (Alpha version)

Introduction to Reproducible Publications with RStudio: Glossary

Key Points

Scientific reproducibility: What is it for?
  • Reproducible research is key for scientific advancement.

  • RStudio can help you to organize, have better control over and produce reproducible research.

Navigating RStudio and R Markdown Documents
  • RStudio has four panes to organize your code and environment.

  • Manage packages in RStudio using specific functions.

  • R Markdown documents combine text and code.

Introduction to Working with R Markdown Files
  • An R Markdown file is comprised of a YAML header, formatted text in Rmd and code chunks.

  • The knit function renders the file into the chosen output format.

  • Rstudio has some journals’ templates that can save you some formatting time or you can make your own for frequent submissions.

Good Practices for Managing Projects in RStudio
  • Use best practices for file and folder organization. This includes using relative file paths as opposed to complete file paths.

  • Make sure that all data are backed up on multiple devices and that you treat raw data as read-only.

  • We can use Git and Github to keep track of what we’ve done in the past, and what we plan to do in the future.

  • Rproj files are pivotal to keeping everything bundled and organized.

Getting Your project set up with Version Control in RStudio
  • R Studio has Git version control functionality built in.

  • Forking a Github repository makes a copy of the repository into your personal account on Github.

  • You can clone a git repository from Github to your local disk using R Studio.

  • For this workshop each learner will work with their own fork of the “R-Repro-pub” repository.

Writing and Styling Rmd Documents
  • The visual editor has made formatting much easier.

  • You can apply Rmd styling without prior R Markdown knowledge.

  • You can include inline code to narratives for basic calculations and dynamic information.

Adding Code-Generated Plots and Figures
  • Knitr will render your code and R markdown-formatted text and output your document format of choice

  • Code chunks are runable piece of R code. Each time you knit the document, calculations and plots will be run and displayed

  • Options for code chunks can be set at the individual level or at the global level

Reproducible & Efficient Methods of Using Code Chunks
  • Learn how to externally source code source()

  • Learn how to modularize your code to make it more reproducible

  • There are options for changing the working directory of your .rmd document with package rprojroot

  • Use a chunk at the beginning of your document to load libraries and data globally to make your document more effiecient.

Bibliography, Citations & Cross-Referencing
  • Rstudio supports different lookups strategies to easy the citation process.

  • Rstudio supports different citation styles.

  • The YAML can be ajusted to display uncited items in the reference list.

  • Use bookdown to cross-reference content.

Collaborating via Github
  • Setting up R Studio to authenticate with Github using a Personal Authentication Token (PAT).

  • Setting the Git repository Origin in your R Studio project enables pushing and pulling from your local copy of the repository to the repository on Github.

Publishing your project
  • You may choose to share and publish your data project before publishing its associated manuscript.

  • Sharing the code, data and documentation is necessary to allow for inspection and research reproducibility.