Reproducible Research

The value of re-analysis

I just saw this really nice post over on John Cook’s blog. He talks about how it is a valuable exercise to re-type code for examples you find in a book or on a blog. I completely agree that this is a good way to learn through osmosis, learn about debugging, and often pick up the reasons for particular coding tricks (this is how I learned about vectorized calculations in Matlab, by re-typing and running my advisors code back in my youth).

Pro Tips for Grad Students in Statistics/Biostatistics (Part 1)

I just finished teaching a Ph.D. level applied statistical methods course here at Hopkins. As part of the course, I gave one “pro-tip” a day; something I wish I had learned in graduate school that has helped me in becoming a practicing applied statistician. Here are the first three, more to come soon.  A major component of being a researcher is knowing what’s going on in the research community.

figshare and don't trust celebrities stating facts

A couple of links: figshare is a site where scientists can share data sets/figures/code. One of the goals is to encourage researchers to share negative results as well. I think this is a great idea - I often find negative results and this could be a place to put them. It also uses a tagging system, like Flickr. I think this is a great idea for scientific research discovery. They give you unlimited public space and 1GB of private space.

Where do you get your data?

Here’s a question I get fairly frequently from various types of people: Where do you get your data? This is sometimes followed up quickly with “Can we use some of your data?” My contention is that if someone asks you these questions, start looking for the exits. There are of course legitimate reasons why someone might ask you this question. For example, they might be interested in the source of the data to verify its quality.

Reproducible Research in Computational Science

First of all, thanks to Rafa for scooping me with my own article. Not sure if that’s reverse scooping or recursive scooping or…. The latest issue of _Science_ has a special section on Data Replication and Reproducibility. As part of the section I wrote a brief commentary on the need for reproducible research in computational science. _Science_ has a pretty tight word limit for it’s commentaries and so it was unfortunately necessary to omit a number of relevant topics.

Reproducible Research and Turkey

Over the Thanksgiving recent break I naturally started thinking about reproducible research in between salting the turkey and making the turkey stock. Clearly, these things are all related. I sometimes get the sense that many people see reproducibility as essentially binary. A published paper is either reproducible, as in you can compute every single last numerical result to within epsilon precision, or it’s not. My feeling is that there is a spectrum of reproducibility when it comes to published scientific findings.