Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
Add a color legend to a phylo-rate plot
Add BAMM-inferred rate shifts to a phylogeny plot
Map macroevolutionary rates to colors
Calculate BAMM likelihood
BAMMtools datasets
BAMMtools
Visualize macroevolutionary cohorts
Compute Bayes Factors
Credible set of macroevolutionary rate shift configurations from `BAMM...
Identify distinct rate shift configurations
Calculate macroevolutionary rate changes on a phylogeny from BAMM ou...
Generate control file for BAMM
Get the best (sampled) rate shift configuration from a BAMManalysis
Compute prior odds of a rate shift on each branch of a phylogeny from ...
Compute clade-specific mean rates
Compute the pairwise correlation in rate regimes between all tips in a...
Create bammdata object from MCMC output
Jenks natural breaks classification
Compute mean branch rates for bammdata object
Compute phylogeny with branch lengths equal to corresponding macroevol...
Find most recent common ancestors
Generate rate-through-time matrix from bammdata object
Identify nodes associated with rate shifts from bammdataobject
Compute tip-specific macroevolutionary rates from bammdataobject
Ratio of (marginal) posterior-to-prior probabilities on individual bra...
Estimate maximum shift credibility configuration
Plot distinct rate shift configurations on a phylogeny
Plot credible set of rate shift configurations from BAMManalysis
Plot BAMM-estimated macroevolutionary rates on a phylogeny
Plot the prior and posterior distribution of shifts
Plot rates through time
Histogram of BAMM rate frequencies
Rich color palette
Creates clade-specific sampling fractions
Set BAMM Priors
Branch-specific rate shift probabilities
Compute species-specific rate through time trajectories
Identify the optimal number of shifts using Bayes factors
Subset a bammdata object
Pulls out a subtree from bammdata object
Summary of rate shift results from BAMM analysis
Summary of credible set of shift configurations from a BAMManalysis
Evaluate evidence for temporal rate variation across tree
STRAPP: STructured Rate Permutations on Phylogenies
Define colors with transparency
Write a bammdata object to disk
Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.