mfabalisi / pyrate

PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.

PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.

The program's documentation is avaiable here:

• Detailed command list: https://github.com/dsilvestro/PyRate/wiki
• Tutorials (work in progress): https://github.com/dsilvestro/PyRate/tree/master/tutorials
• For questions, suggestions or bugs contact us

The main methods are described here:

• 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.

• 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 MCDD model is described here:

• 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., Pires M. M., Quental T., Salamin N. Bayesian estimation of multiple clade competition from fossil data. Evolutionary Ecology Research, 17, early edition.

The DES method is described here:

• 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. R. Soc. B 371: 20150225, in press.