ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix

The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.

Version: 1.2.4
Depends: R (≥ 3.5.0)
Imports: ape, geiger, coda, corpcor, MASS, phylolm, readr, mvMORPH, Rcpp, ellipse
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, phytools, markdown
Published: 2022-06-03
DOI: 10.32614/CRAN.package.ratematrix
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
CRAN checks: ratematrix results


Reference manual: ratematrix.pdf
Vignettes: Introdution to ratematrix
Using prior distributions
Set custom starting point


Package source: ratematrix_1.2.4.tar.gz
Windows binaries: r-devel: ratematrix_1.2.4.zip, r-release: ratematrix_1.2.4.zip, r-oldrel: ratematrix_1.2.4.zip
macOS binaries: r-release (arm64): ratematrix_1.2.4.tgz, r-oldrel (arm64): ratematrix_1.2.4.tgz, r-release (x86_64): ratematrix_1.2.4.tgz, r-oldrel (x86_64): ratematrix_1.2.4.tgz
Old sources: ratematrix archive


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