Research Transparency & Reproducibility Training (RT2)
Materials for workshop on research transparency, Los Angeles 2018
The workshop will introduce you to a tool that can help you make your workflow more reproducible: version control (Git/GitHub). You are required to install the following software programs either on your personal laptop before coming to the workshop for the hands-on exercises. (please remember to bring the laptop too!)
1. Version Control with Git and the Github Desktop app
Version control is a powerful way to carefully track revisions to your documents as well as to manage collaboration. Git and Github Desktop are packaged together here. Git is the command line tool, and Github Desktop is a GUI version of the same tool.
There are actually a whole bunch of GUI apps that can act as front ends, so you might find later that you prefer another, but we'll stick with Github Desktop for the demo.
Optional: Specifics for Specifics Platforms
Note that Github Desktop works on Mac and Windows. If you're a Linux user, you might try one of these. Also if you're a Windows user, the command line tool that comes with Github Desktop is not the greatest, so you might want to download this alternative. If you've never used the command line before or any of this is confusing, don't worry about it and we'll try to clear it up at the workshop.
2. A good text editor
Writing good code is facilitated by a good text editor. You can get away without one because you almost certainly already have a program on your computer that can save simple ASCII text files (Notepad for Windows, or TextEdit for Mac--but change the default from Rich Text to Plain Text) but modern text editors do syntax highlighting, auto-complete, and a bunch of other cool stuff for you. I suggest Atom. You can extend its functionality by going to settings and adding packages (one to render Markdown as PDF might be especially helpful.)
3. Install R and RStudio
If you have downloaded R or RStudio, make sure that your version is up to date.
Open RStudio and click on the following
File-> New File -> RMarkdown..., when prompted to install additional packages, click yes.
4. Install LaTeX
If you could not install LaTeX previously, run the following 2 lines of code in the RStudio console: