UO Advanced Biological Statistics

Course development

Debugging the html

To view a local version install jekyll and run jekyll serve.

Git and github

Branches

If you want to push to github but don’t want to break everything, make a new branch, and then if you want to discuss the changes with others, make a pull request. To do this,

  1. Checkout a new branch, which you can call whatever you want (eg my_new_branch): 
     git checkout -b my_new_branch

  2. Make your changes. Commit them. You can make as many commits as you like.

  3. Push the changes to a new branch on github 
     git push --set-upstream origin my_new_branch

  4. Go to the github repo. If you are logged in, it will helpfully ask you if you want to start a new pull request from the branch you just pushed. Yes, please! Write something so the rest of us know what we’re looking at; this gives us a space to comment and discuss.

  5. Now, we discuss and comment; push more changes to the branch, etcetera. And, eventually, merge it to master.

  6. When it’s merged, switch back to master and delete the now-unused branch: 
     git checkout master
 git fetch
 git merge origin/master
 git branch -d my_new_branch

Note: If you want to switch back to master temporarily, this is as easy as doing git checkout master; having a look, and then git checkout my_new_branch to get back.

Rmarkdown

The Rmarkdown slides can be knitted from Rstudio, but I don’t do it that way. Here’s how I do it:

  1. install templater, which is a small R package I wrote as a wrapper around knitr and pandoc

    Note: what knitr does is it first evaluates code chunks and makes a .md file; then it calls pandoc to make the html.

  2. to make a certain set of slides, run e.g. make Week_03_Lecture.slides.html. Running this will do these two things: 
    Rscript -e 'knitr::knit_patterns[["set"]](list( chunk.begin="^```+\\s*\\{[.]?(r[a-zA-Z]*.*)\\}\\s*$", chunk.end="^```+\\s*$", inline.code="`r +([^`]+)\\s*`")); templater::render_template("Week_03_Lecture.Rmd", output="Week_03_Lecture.md", change.rootdir=TRUE)'
pandoc -o Week_03_Lecture.slides.html -t revealjs -V theme=simple -V slideNumber=true -V transition=none -H resources/adjust-revealjs.style --slide-level 2 --standalone  --self-contained -H .pandoc.macros.tex --mathjax=https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML  Week_03_Lecture.md

    There is, for instance, some special CSS configuration to the slides in resources/adjust-revealjs.style.

  3. To run the R code in a console, to do for instance online examples, open R and then run: 
    library(templater)
render_template("Week_03_Lecture.Rmd", envir=environment(), output="Week_03_Lecture.md")

    This says to knit the Rmd document in the current environment, so all the variables are available, and output just the markdown file instead of going all the way to html.