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.
Last updated 2 years ago
5.86 score 9 stars 1 packages 18 scripts 219 downloadsdo3PCA - Probabilistic Phylogenetic Principal Component Analysis
Estimates probabilistic phylogenetic Principal Component Analysis (PCA) and non-phylogenetic probabilistic PCA. Provides methods to implement alternative models of trait evolution including Brownian motion (BM), Ornstein-Uhlenbeck (OU), Early Burst (EB), and Pagel's lambda. Also provides flexible biplot functions.
Last updated 2 months ago
1.00 score 241 downloads