Generating reproducible, dynamic documents

September 14, 2020 • PD Schloss • 1 min read • •

You can find my version of the project on GitHub.

Important things to remember

• GitHub flavored markdown
• R markdown
  • cheat sheet
  • website
  • book
• Code chunk options
  • echo (TRUE or FALSE): whether to include the code in the rendered file
  • message (TRUE or FALSE): whether to include any messages generated by commands (e.g. library(tidyverse))

Installations

If you haven’t been following along, you can get caught up by doing the following:

• (windows) Install the Ubuntu Linux BASH shell for Windows 10
• (mac) Install homebrew and wget

    /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
    brew install wget
  

• To get to where we are at the beginning of this episode (you won’t have the same issue numbers at Pat)…
  • Set up a GitHub account
  • Create a new GitHub repository
    • Call it “Schloss_rrnAnalysis_XXXX_2020” (feel free to use your own last name)
    • Make it Public
    • Don’t check the box next to “Initialize this repository with a README”
    • Click the green “Create repository” button

  • Go to your command line and enter the following replacing <your_github_id> with your GitHub user id

    git clone git@github.com:SchlossLab/Schloss_rrnAnalysis_mSphere_2020.git
    cd Schloss_rrnAnalysis_XXXX_2020
    git reset --hard a4ade7f42
    git remote set-url origin git@github.com:<your_github_id>/Schloss_rrnAnalysis_XXXX_2020.git
    git push -u origin master
    

  • Return to GitHub and refresh your browser. Then you’ll be good to go.