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BAMMtools (version 2.1.1)

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

1,455

Version

2.1.1

License

GPL (>= 2)

Maintainer

Pascal Title

Last Published

March 3rd, 2016

Functions in BAMMtools (2.1.1)

getRateThroughTimeMatrix

Generate rate-through-time matrix from bammdata object

BAMMtools-package

BAMMtools-internal

Internal BAMMtools functions

getMeanBranchLengthTree

Compute phylogeny with branch lengths equal to corresponding macroevolutionary rate estimates

Create bammdata object from MCMC output

Visualize macroevolutionary cohorts

Calculate BAMM likelihood

Add a color legend to a phylo-rate plot

getShiftNodesFromIndex

Identify nodes associated with rate shifts from bammdata object

distinctShiftConfigurations

Identify distinct rate shift configurations

getBranchShiftPriors

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

Find most recent common ancestors

subsetEventData

Subset a bammdata object

Compute clade-specific mean rates

plot.credibleshiftset

Plot credible set of rate shift configurations from BAMM analysis

traitDependentBAMM

STRAPP: STructured Rate Permutations on Phylogenies

generateControlFile

Generate control file for BAMM

getBestShiftConfiguration

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

Add BAMM-inferred rate shifts to a phylogeny plot

Calculate macroevolutionary rate changes on a phylogeny from BAMM output

Creates clade-specific sampling fractions

Jenks natural breaks classification

Pulls out a subtree from bammdata object

Compute tip-specific macroevolutionary rates from bammdata object

credibleShiftSet

Credible set of macroevolutionary rate shift configurations from BAMM results

marginalOddsRatioBranches

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

transparentColor

Define colors with transparency

summary.credibleshiftset

Summary of credible set of shift configurations from a BAMM analysis.

speciesByRatesMatrix

Compute species-specific rate through time trajectories

maximumShiftCredibility

Estimate maximum shift credibility configuration

Branch-specific rate shift probabilities

Plot the prior and posterior distribution of shifts

computeBayesFactors

computeBayesFactors

assignColorBreaks

Map macroevolutionary rates to colors

getMarginalBranchRateMatrix

compute mean branch rates for bammdata object

Write a bammdata object to disk

BAMMtools datasets

Histogram of BAMM rate frequencies

summary.bammdata

Summary of rate shift results from BAMM analysis.

plot.bammshifts

Plot distinct rate shift configurations on a phylogeny

plotRateThroughTime

Plot rates through time

getCohortMatrix

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

testTimeVariableBranches

Evaluate evidence for temporal rate variation across tree

Plot BAMM-estimated macroevolutionary rates on a phylogeny