ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix

Estimates the evolutionary rate matrix (R) using Markov chain Monte Carlo (MCMC) as described in Caetano and Harmon (2017) <doi:10.1111/2041-210X.12826>. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.

Version: 1.0
Depends: R (≥ 2.10)
Imports: ape, geiger, coda, corpcor, MASS, phylolm, readr, mvMORPH, Rcpp, ellipse
LinkingTo: Rcpp, RcppArmadillo
Suggests: microbenchmark, knitr, rmarkdown, phytools
Published: 2018-06-10
Author: Daniel Caetano [aut, cre], Luke Harmon [aut]
Maintainer: Daniel Caetano <caetanods1 at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2.0)]
URL: https://github.com/Caetanods/ratematrix
NeedsCompilation: yes
Materials: README
In views: Phylogenetics
CRAN checks: ratematrix results

Downloads:

Reference manual: ratematrix.pdf
Vignettes: Using prior distributions
Set custom starting point
Package source: ratematrix_1.0.tar.gz
Windows binaries: r-devel: ratematrix_1.0.zip, r-release: ratematrix_1.0.zip, r-oldrel: ratematrix_1.0.zip
OS X binaries: r-release: ratematrix_1.0.tgz, r-oldrel: not available

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