In benmarwick/pyrater: Estimate Speciation, Extinction, and Preservation Rates

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pyrater

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.

How to install

You can install this package by running this line:

devtools::install_github("benmarwick/pyrater")

Prerequisites

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.

Relevant publications

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) doi:10.1057/palcomms.2016.19

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, doi:10.1111/nph.13247.

benmarwick/pyrater documentation built on May 7, 2019, 10:38 a.m.