The goal of pyrater is to give R users access to Daniele Silvestro's PyRate, a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
You can install this package by running this line:
devtools::install_github("benmarwick/pyrater")
You need to have Python 2.7 installed on your machine to use the functions in PyRate. You can download Python 2.7 from https://www.python.org/download/releases/2.7/. You will also need numpy and scipy.
Gjesfjeld, E., Chang, J., Silvestro, D., Kelty, C., & Alfaro, M. (2016). Competition and extinction explain the evolution of diversity in American automobiles. PALGRAVE COMMUNICATIONS 2, Article number: 16019 (2016)
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.
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, .
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