Tuesday, March 6, 2012

Presenting: paleotree v1.2

Hello all,
After more than month of having my library up on CRAN and finally feeling satisfied that I've worked out enough of the bugs, I'd like to introduce you to my R library, paleotree! It does many things, but if you like phylogenetics, fossils and particularly the overlap of those two, you may find something in interest! With paleotree, you can time-scale cladograms of fossil taxa, estimate sampling rates from the ranges of fossil taxa, plot diversity curves and simulate diversification and sampling in the fossil record. So, go download version 1.2 and check it out! The entire library will be described in a paper I submitted a week and a half ago to Methods in Ecology and Evolution and apparently is now in review. I'll add a citation file to paleotree when that gets more definite. Until then, cite Bapst, D. (in review)!


Now, I would like to note that some of the included functions, such as the sampling-rate conditioned time-scaling methods, are not described yet in the primary literature. The methods are included in the current release and you can use them if you wish, but Buyer Beware and all that. The algorithm behind these methods will be described in more detail in a future. For the moment, I would actually suggest you use the more typical time-scaling methods, applicable with timePaleoPhy and bin_timePaleoPhy.

Let me know if you run into any bugs! You can find my email address in the help files for R if you don't know it already. Also, I have tried to be very meticulous with regards to the help files and tried to make them as clear as possible, but I am sure my general muddled-ness will show through. So, if you don't understand anything, let me know so I can clarify the help files in the next release!

So far, in terms of potential errors and bugs in version 1.2, I have discovered that simFossilTaxa can enter an infinite loop under some parameter choices if you try a pure-birth model. I don't know why you'd want to do a pure-birth simulation of the fossil record, but this will be fixed in the next release. Then you can simulate your extinction-less fossil record to your heart's content!

Finally, let me know if you get any good ideas of what I could add that would make analyses in phylogenetic paleobiology easier for you!

-Dave B.