Saturday, July 10, 2010

Open source: doing my bit

Although I can hardly claim to be a prolific blogger I do visit this page regularly to look for updates of other people's blogs (see list at left). One of these (The Open Source Paleontologist) is concerned with the public availability of both data and primary literature. Needless to say I agree with much of what is written there. As many of my readers wll know I also maintain my own site:, where I try and do my bit. As is often the way with these things my ambition for what should be there goes well beyond my actual motivation to produce it. However, there is some stuff that people apparently do find useful and prompted by some recent comments I thought I'd take an opportunity to advertise what is there for those that haven't visited.

1. Dinosaur supertree bonus material

First off there is extra data from my dinosaur supertree paper, produced with my colleagues over at Raptor's Nest and Museological Meanderings. This includes the MRP matrices (as NEXUS files), the original tree and XML files, as well as R source code for the subsampling analyses. Apparently somebody has used this code so it was worthwhile!

2. Dinosaur matrix list

In conjunction with the above I have been collating a list of published cladistic analyses of dinosaurs. Many of these come from the supertree project, but I have kept an eye out for more recent things and just yesterday updated my list, so presently it is current. I also include NEXUS files of the matrices plus MPTs where I've had time to produce them. Again, this list has been used by at least a few people, but I have no doubt there are publications I've missed so for those keen enough to point them out I would be glad of the info. My eventual aim is to produce a proper relational database that allows automated creation of MRP files and hence an "instant" up-to-date formal supertree of the group.

3. Tree dating code

I wrote a post a while back about the problem of dating phylogenetic trees of fossil taxa. I subsequently wrote code to do it in R and know a lot of people already use it. There are plans to include this with some other functions in a full-fledged library - watch this space.

4. Palaeo-polygon area

I have also written some code to measure the area of the polygon described by the convex hull of a bunch of palaeolatitude and longitudes (now available as a downloadable field in the PaleoDB). Again, this was prompted by an old post. However, it should be noted that there are issues with this function. I now have it working better, but have yet to update the page (email me if you're desperately interested and I'll give you the latest one).

5. Red Queen PDF

On a trip to Chicago where I interviewed for their PhD program I was able to get my hands on Leigh Van Valen's ridiculously well cited, but poorly read Red Queen paper. As I got asked for this a lot I ended up scanning it in and making an OCR'd PDF and have made this available (with permission).

6. Endnote libraries for edited volumes

Being of a macroevolutionary bent I have a large personal library and spent a good chunk of my PhD entering everything into Endnote. Services like WoK were great for entering my journal runs of Palaeontology and JVP (I could just download everything from between a starting year to present), but no such electronic resource exists for my several edited books. These I had to enter manually, at no little effort. It seemed prudent then, to make these freely available once I was done and so you can browse and download copies from this page. I ended up using BibTeX for my thesis in the end and so hope to one day add this format too. I have also added links to these volumes on Amazon (if you buy via this link I get money!) and a bookfinder search (which will usually be cheaper, probably why I haven't made any yet).

Well, that's it for now. Hopefully some of you find at least one of these things useful. It is gratifying to me to know people are using it so please let me know if you like it or if there is anything else you'd like to have. After all, blogs are supposed to be interactive, right?

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About Me

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Currently I am founding member, president elect and entire membership of SWEMP (the Society of Wonky-Eyed Macroevolutionary Palaeobiologists). In my spare time I get paid to do research on very dead organisms and think about the really big questions in life, such as: What is the ultimate nature of reality? Why is there no room for free will in science? and What are the implications of having a wardrobe that consists entirely of hotpants?