P2C2M conducts posterior predictive checks of coalescent models using gene and species trees generated by 'BEAST' or '*BEAST'. It was designed to be as accurate and user-friendly as possible.
To install P2C2M, first download the gunzipped tarball and then install from source in R with:
r install.packages("path/to/P2C2M_1.0.0.tar.gz", repos = NULL, type = "source")
R (>=3.0.0), ape (>=3.1-4), ggplot2 (>=1.0.0), rPython (>=0.0-5), stringr (>=0.6.2), phybase (>=1.3.1) - not on CRAN, Rmpi (>=0.6-5), xtermStyle (>=2.2-4),
Python (>=3.5.0), dendropy (>=3.12.0), numpy (>=1.9.0)
The P2C2M package contains a single function, p2c2m.complete. It requires as input the tree, log, and .xml files from a '*BEAST' analysis. The function will read the inut values, extract tree and metadata parameters, simulate new datasets, calculate summary statistics for each dataset, and compare simulated datasets to the empirical dataset to identify model violations. Simulations use Richard Hudson's ms software. A full tutorial is available from the P2C2M GitHub page [https://github.com/P2C2M]
Please cite P2C2M as: Gruenstaeudl, M., Reid, N. M., Wheeler, G. L., & Carstens, B. C. (2016). Posterior predictive checks of coalescent models: P2C2M, an R package. Molecular ecology resources, 16(1), 193-205.