September Scientiae

September’s Scientiae is up now at Ruminations of an Aspiring Ecologist.  Karina asked us what kinds of tools we use and got a lot of fun answers.  It was also fun to see what “school supplies” many of us had in common.

Like Eugenie and Rocksinspace, I find Mendeley to be a lifesaver.  It’s free, syncs between computers and the web, and does everything from organizing my crazy collection of pdfs to inserting citations as I write.  It’s what I wanted Papers to be and what Sente tries – and fails – to be.

I am 100% with Mariawolters on using R for statistical modeling and analysis.  While it’s been the source of many, many tantrums, I couldn’t do without it.  Like Mariawolters puts it:

R is a programming language for everything statistical. It’s free, it’s open source, and it’s being maintained by statisticians for statisticians. Its origin means that it is a pain to learn. It takes a while until one has cleared a path through the data structures, including the various conventions for extracting information from objects that store the results of painstaking statistical analyses, and I am still often baffled myself.

But the payoff is magnificent. Clear (modulo coding ability), open, replicable analyses. R is the ultimate in replicable research. If you give people your data set and your source code, they can repeat every single step of your reasoning. There are no paywalls, no limits of affordability, no packages that are indispensable for the analysis, but that your department hasn’t paid for.