R pitfall #3: friggin’ factors

I received an email from one of my students expressing deep frustation with a seemingly simple problem. He had a factor containing names of potato lines and wanted to set some levels to NA. Using simple letters as example names he was baffled by the result of the following code:

The factor has been… Continue reading R pitfall #3: friggin’ factors

Lattice when modeling, ggplot when publishing

When working in research projects I tend to fit several, sometimes quite a few, alternative models. This model fitting is informed by theoretical considerations (e.g. quantitative genetics, experimental design we used, our understanding of the process under study, etc.) but also by visual inspection of the data. Trellis graphics—where subsets of data are plotted in… Continue reading Lattice when modeling, ggplot when publishing

Upgrading R (and packages)

I tend not to upgrade R very often—running from 6 months to 1 year behind in version numbers—because I had to reinstall all packages: a real pain. A quick search shows that people have managed to come up with good solutions to this problem, as presented in this stackoverflow thread. I used the code in… Continue reading Upgrading R (and packages)