PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
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Silvestro D., Schnitzler J., Liow L.H., Antonelli A. and Salamin N. (2014) Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Systematic Biology, 63, 349-367.
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Silvestro D., Salamin N., Schnitzler J. (2014) PyRate: A new program to estimate speciation and extinction rates from incomplete fossil record. Methods in Ecology and Evolution, 5, 1126-1131.
The program's manual is available here: https://github.com/dsilvestro/PyRate/wiki.
The model with fixed shift times and Cauchy hyper-priors on the birth-death rates is described here:
- Silvestro D., Cascales-Minana B., Bacon C. D., Antonelli A. (2015) Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. New Phytologist, 207, 425-436.
- Silvestro D., Antonelli A., Salamin N., Quental T. B. (2015) The role of clade competition in the diversification of North American canids. PNAS, 112, 8684-8689.
- Silvestro, D., Zizka A., Bacon C. D., Cascales-Minana B. and Salamin, N., Antonelli, A. (2016) Fossil Biogeography: A new model to infer dispersal, extinction and sampling from paleontological data. Phil Trans Roy Soc B, in press.