Reproducible Research Reporting with R and RStudio

• Maintainers: Tom Morrell
• Lesson Content: Gail Clement, Tom Morrell, Donna Wrublewski, Robert Doiel, Yuvi Panda

Lesson status: In Development

What you will learn:

• Identify the features of a reproducible and dynamic research report that is fit to enter the scholarly record.
• Describe the benefits of composing research reports with open authoring tools in RStudio.
• Apply an open, text-based workflow for creating a paper that combines dynamic text, code and software.
• Use the Rmarkdown-Knitr-Pandoc workflow to convert openly authored documents for publication, online posting and professional presentation.
• Demonstrate use of the RStudio GUI platform for authoring and producing professional-quality research reports.

Topics:

1. Introduction
2. Basic Markdown
3. Document Appearance
4. Dynamic Documents
5. Publishing

Requirements

Author Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to insure the proper setup of tools for an efficient workflow. These lessons assume no prior knowledge of the skills or tools, but working through this lesson requires working copies of R and Rstudio.

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio. For this workshop you’ll need to install both R (version 3.4.3 or newer) and RStudio on your computer. Please follow these installation instructions before coming to the workshop

Windows

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select “Run as administrator” instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

macOS

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.

Workshop Files

You also need to download some files for this workshop. Extract this folder and put it on your desktop. This is where we will be working throughout the workshop.