Download Latest Version
README.txt (2.1 kB)
Get an email when there's a new version of PyRate
| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| Hesperocyoninae.py | 2015-09-05 | 300.5 kB | |
| info.txt | 2015-09-01 | 281 Bytes | |
| Amphicyonidae.py | 2015-09-01 | 166.3 kB | |
| Barbourofelidae.py | 2015-09-01 | 26.6 kB | |
| Borophaginae.py | 2015-09-01 | 883.6 kB | |
| Caninae.py | 2015-09-01 | 370.1 kB | |
| Carnivores_MCDD.txt | 2015-09-01 | 781.2 kB | |
| Felidae.py | 2015-09-01 | 337.7 kB | |
| Nimravidae.py | 2015-09-01 | 71.9 kB | |
| Ursidae.py | 2015-09-01 | 214.0 kB | |
| Totals: 10 Items | 3.2 MB | 0 | |
============================================================
PyRate
version 0.580, May 2015
============================================================
General Info
----------------------------------------
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.
Manual and example files can be found here: https://sourceforge.net/projects/pyrate/, a Wiki page is also under construction: https://github.com/dsilvestro/PyRate/wiki.
The latest version of PyRate can be downloaded here: https://github.com/dsilvestro/PyRate/.
Compatibility and requirements
----------------------------------------
PyRate has been tested under Unix operating systems (Mac OS 10.6 or higher and Cent OS 6) and under Windows (XP and 7) using Python 2.6 - 2.7. The program requires the library argparse, which needs to be installed manually under Python 2.6 (it can be found here: https:// code.google.com/p/argparse/), whereas it is part of the default installation in Python 2.7.
Please note that Python 3.x is currently not supported, Python 2.7.x can be found here: https:// www.python.org/downloads/.
The libraries numpy and scipy are required. Source files and installers are available here: http:// sourceforge.net/projects/numpy/files/ and http://sourceforge.net/projects/scipy/files/. Under UNIX systems, PyRate will use the library multiprocessing and thread (if available) and implement parallel computation of the likelihoods (see command -thread).
Contacts
----------------------------------------
Please report suggestions and bugs to:
pyrate.help[at]gmail.com
