This repository includes Bayesian implementations of the MuSSE and ClaSSE methods. The use of (half-Cauchy or Exponential) hyper-priors on the rate parameters allows to control for overparameterization.
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README.md
mcmc-musseCauchy.R
mcmc-musseExp.R

README.md

mcmc-diversitree

This repository includes Bayesian implementations of the MuSSE and ClaSSE methods. The use of (half-Cauchy or Exponential) hyper-priors on the rate parameters allows to control for overparameterization.

Requirements

R libraries: ape, optparse, picante, diversitree all available at https://cran.r-project.org.

References

The diversitree library:
http://sysbio.oxfordjournals.org/content/58/6/595
https://github.com/richfitz/diversitree

mcmc-diversitree:
http://onlinelibrary.wiley.com/doi/10.1111/evo.12236/abstract
http://www.nature.com/ncomms/2016/160407/ncomms11250/full/ncomms11250.html