Reproducibility in computational research

Jane Frazier spoke at our research team meeting today on “Reproducibility in computational research”. We had a very stimulating and lively discussion about the issues involved. One interesting idea was that reproducibility is on a scale, and we can all aim to move further along the scale towards making our own research more reproducible. For example

  • Can you reproduce your results tomorrow on the same computer with the same software installed?
  • Could someone else on a different computer reproduce your results with the same software installed?
  • Could you reproduce your results in 3 years time after some of your software environment may have changed?
  • etc.

Think about what changes you need to make to move one step further along the reproducibility continuum, and do it.

Jane’s slides and handout are below. Continue reading →

Mathematical annotations on R plots

I’ve always struggled with using plotmath via the expression function in R for adding mathematical notation to axes or legends. For some reason, the most obvious way to write something never seems to work for me and I end up using trial and error in a loop with far too many iterations.

So I am very happy to see the new latex2exp package available which translates LaTeX expressions into a form suitable for R graphs. This is going to save me time and frustration! Continue reading →

Dark themes for writing

I spend much of my day sitting in front of a screen, coding or writing. To limit the strain on my eyes, I use a dark theme as much as possible. That is, I write with light colored text on a dark background. I don’t know why this is not the default in more software as it makes a big difference after a few hours of writing.

Most of the time, I am writing using either Sublime Text, RStudio or TeXstudio. Each of them can be set to use a dark theme with syntax coloring to highlight structural features in the text.
Continue reading →

Creating a handout from beamer slides

I’m about to head off on a speaking tour to Europe (more on that in another post) and one of my hosts has asked for my powerpoint slides so they can print them. They have made two false assumptions: (1) that I use powerpoint; (2) that my slides are static so they can be printed.

Instead, I produced a cut-down version of my beamer slides, leaving out some of the animations and other features that will not print easily. Then I produced a pdf file with several slides per page. Continue reading →

Generating tables in LaTeX

Typing tables in LaTeX can get messy, but there are some good tools to simplify the process. One I discovered this week is, a web-based tool for generating LaTeX tables. It also allows the table to saved in other formats including HTML and Markdown. The interface is simple, but it does most things. For complicated tables, some additional formatting may be necessary. Continue reading →