Biostatistics in practice workshop at MGHPCC

Last Friday, 11/07/14, I attended the “Biostatistics in Practice” workshop at the Massachusetts Green High Performance Computing Center (or MGHPCC), which was organized by the department of biostatistics, UMass Amherst.

Front side of the MGHPCC main building

What was cool about it? Pretty much everything! 😀 Here’s a small summary of the things I learned there.

  • There is a way to include R code (or from almost any other language, really) in a document, pass that document through TeX or Markdown and generate a pdf or html file that has both your text, the code and the results of the code after it is run. In other words, you can generate graphs directly from within TeX or Markdown. This can be done with a tool called knitr which can be used either from R-studio or from another editor.
  • That R-studio is a great IDE to work on. And not just for R but also when working on TeX or Markdown files. I noticed that you can write TeX expressions within an R-markdown file and when you convert it into html, the html file uses MathJax to render all the formulas.
  • How to use git as a tool for collaboration and reproducible research.
  • Various stuff on how to use and access the MGHPCC cluster.

I may be forgetting other stuff as well. That’s OK though, since the presenters, Nicholas Reich, Gregory Matthews (who also has a blog here at WordPress) and Andrea Foulkes have made all of the material used available on Github. Grab it from here.

I really think that those kinds of workshops is something that should happen more often. There are times when we are doing something and it takes a lot of time, so then we start to think, “is that really how other people do this?”

Knitr is certainly a nice answer to that question. 🙂