This project is archived on zenodo:
This repository serves as an open-science notebook for research conducted by Jamie Oaks, Charles Linkem, Jeet Sukumaran, and others into Bayesian methods of phylogeographcial model choice. We use simulated and biological data to assess the behavior of existing and newly developed methods for estimating the probability of models of shared divergence times across a set of co-distributed populations.
Replicating our work will require a unix shell and Python. Specifically, we conducted the work using bash and Python version 2.7.
Also, most of the heavy lifting was performed using the Python package
PyMsBayes, which should work in
Linux and Mac OsX.
An archive of the PyMsBayes code
repository that will reproduce all our results is included in top-level
directory software-archive.
If you want to go so far as to generate the plots used in the manuscripts and
slides, you will also need the Python plotting library
matplotlib.
If you want to compile PDFs of manuscripts and slides, you will also need
LaTeX.
All of the analyses we performed for this open-science notebook are sparsely documented. This lack of ``in-text'' documentation is purposeful; the fine-grained commit history (and associated comments) of the git repository is a much more detailed, accurate, and useful guide to the step-by-step progress of this project. Thus, the history of this repository is meant to be the primary guide for reproducing our work.
This project was made possible by funding provided to Jamie Oaks from the National Science Foundation (DEB 1011423 and DBI 1308885), University of Kansas (KU) Office of Graduate Studies, Society of Systematic Biologists, Sigma Xi Scientific Research Society, KU Ecology and Evolutionary Biology Department, and the KU Biodiversity Institute.
This work is licensed under a Creative Commons Attribution 4.0 International License.
