| File | Date | Author | Commit |
|---|---|---|---|
| old_or_experimental_code | 2015-07-22 |
dsilvestro
|
[4e85de] MCDD model with horseshoe prior instead of BVS |
| pyrate_lib | 2015-07-22 |
dsilvestro
|
[072ce7] new option in calc_marginal_likelihood function |
| PyRate.py | 2015-07-22 |
dsilvestro
|
[6dadb5] fixed marginal rates and RTT for long extinct c... |
| PyRateContinuous.py | 2015-05-19 |
dsilvestro
|
[cf4a49] added function to calculate marginal likelihood |
| PyRateMCDD.py | 2015-07-22 |
dsilvestro
|
[df9c28] added flags and non-uniform priors on indicators |
| README.md | 2015-07-22 |
dsilvestro
|
[f4e351] updated references |
| pyrate_utilities.r | 2014-10-29 |
Jan Schnitzler
|
[2b2d20] added additional check of input file structure |
| tempPyRate.txt | 2014-08-06 |
dsilvestro
|
[b164f9] MCC model - Silvestro et al in prep. |
PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. The method was 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.
An updated manual is available here: https://github.com/dsilvestro/PyRate/wiki. A PDF manual (no longer updated) and example files can be found here: https://sourceforge.net/projects/pyrate/.
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.
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.
