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PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. The methods and the program are described here:
Silvestro, D., Schnitzler, J., Liow, L.H., Antonelli, A. & 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
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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).
To launch a PyRate analysis on UNIX browse via Terminal to the PyRate directory and type:
./PyRate.py path_to_input_file/file_name.py [commands]
or
python PyRate.py path_to_input_file/file_name.py [commands]
To start PyRate on Windows, browse via Command prompt to the PyRate directory and type:
python PyRate.py path_to_input_file/file_name.py [commands]
If you are working under Windows, please make sure that the path to python.exe is included in the PATH environment variables. To do so, edit the PATH environment variable and add the folder in which Python 2.x is installed (e.g. ‘C:\python27’). An easy tutorial how to do that can be found for example on the Java website: https://www.java.com/en/download/help/path.xml
The function -plot generates an R script that is used to produce a graphic output. The script is automatically executed by PyRate using the shell command RScript. If you are working under Windows, please make sure that the path to Rscript.exe is included in the PATH environment variables (default in Mac/Linux). To do so, edit the PATH environment variable and add the \bin\ folder of the R installation (e.g. ‘C:\Program Files\R\R-2.14.0\bin\i386’). An easy tutorial how to do that can be found for example on the Java website: https://www.java.com/en/download/help/path.xml
The R script pyrate_utilities.r was tested under R version 2.x and 3.x. The function fit.prior requires the package fitdistrplus.