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BAMMtools (version 2.1.11)

Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

Description

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.

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Version

Install

install.packages('BAMMtools')

Monthly Downloads

1,579

Version

2.1.11

License

GPL (>= 2)

Maintainer

Pascal Title

Last Published

December 19th, 2023

Functions in BAMMtools (2.1.11)

getCohortMatrix

Compute the pairwise correlation in rate regimes between all tips in a bammdata object

Create bammdata object from MCMC output

generateControlFile

Generate control file for BAMM

getShiftNodesFromIndex

Identify nodes associated with rate shifts from bammdata object

Visualize macroevolutionary cohorts

getBranchShiftPriors

Compute prior odds of a rate shift on each branch of a phylogeny from BAMM output

assignColorBreaks

Map macroevolutionary rates to colors

Compute clade-specific mean rates

maximumShiftCredibility

Estimate maximum shift credibility configuration

Plot BAMM-estimated macroevolutionary rates on a phylogeny

Compute tip-specific macroevolutionary rates from bammdata object

Add BAMM-inferred rate shifts to a phylogeny plot

Add a color legend to a phylo-rate plot

Calculate macroevolutionary rate changes on a phylogeny from BAMM output

distinctShiftConfigurations

Identify distinct rate shift configurations

speciesByRatesMatrix

Compute species-specific rate through time trajectories

testTimeVariableBranches

Evaluate evidence for temporal rate variation across tree

Identify the optimal number of shifts using Bayes factors

traitDependentBAMM

STRAPP: STructured Rate Permutations on Phylogenies

Find most recent common ancestors

Pulls out a subtree from bammdata object

getBestShiftConfiguration

Get the best (sampled) rate shift configuration from a BAMM analysis

subsetEventData

Subset a bammdata object

Creates clade-specific sampling fractions

Set BAMM Priors

marginalOddsRatioBranches

Ratio of (marginal) posterior-to-prior probabilities on individual branches

getMeanBranchLengthTree

Compute phylogeny with branch lengths equal to corresponding macroevolutionary rate estimates

getRateThroughTimeMatrix

Generate rate-through-time matrix from bammdata object

Rich color palette

Histogram of BAMM rate frequencies

summary.bammdata

Summary of rate shift results from BAMM analysis

summary.credibleshiftset

Summary of credible set of shift configurations from a BAMM analysis

Jenks natural breaks classification

computeBayesFactors

Compute Bayes Factors

credibleShiftSet

Credible set of macroevolutionary rate shift configurations from BAMM results

plot.bammshifts

Plot distinct rate shift configurations on a phylogeny

getMarginalBranchRateMatrix

Compute mean branch rates for bammdata object

Plot the prior and posterior distribution of shifts

plot.credibleshiftset

Plot credible set of rate shift configurations from BAMM analysis

plotRateThroughTime

Plot rates through time

transparentColor

Define colors with transparency

Write a bammdata object to disk

Calculate BAMM likelihood

BAMMtools datasets

cumulativeShiftProbsTree

Branch-specific rate shift probabilities