P2C2M (version 0.7.6)

P2C2M-package: Posterior Predictive Checks of Coalescent Models

Description

P2C2M provides functions to read default output from BEAST (Drummond and Rambaut 2007) and *BEAST (Heled and Drummond 2010) and conduct posterior predictive checks of coalescent models (Reid et al. 2014) with the help of data simulation and summary statistics under various settings.

References

Drummond, A.J. and Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.

Gruenstaeudl, M., Reid, N.M., Wheeler, G.R. and Carstens, B.C., submitted. Posterior Predictive Checks of Coalescent Models: P2C2M, an R package.

Heled, J. and Drummond, A.J. (2010) Bayesian inference of species trees from multilocus data. Molecular Biology And Evolution, 27, 570--580.

Reid, N.M., Brown, J.M., Satler, J.D., Pelletier, T.A., McVay, J.D., Hird, S.M. and Carstens, B.C. (2014) Poor fit to the multi-species coalescent model is widely detectable in empirical data. Systematic Biology, 63, 322--333.