Learn R Programming

⚠️There's a newer version (2.1.12) of this package.Take me there.

BAMMtools (version 2.1.6)

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.

Copy Link

Version

Install

install.packages('BAMMtools')

Monthly Downloads

1,181

Version

2.1.6

License

GPL (>= 2)

Maintainer

Pascal Title

Last Published

February 3rd, 2017

Functions in BAMMtools (2.1.6)

BAMMtools datasets

distinctShiftConfigurations

Identify distinct rate shift configurations

assignColorBreaks

Map macroevolutionary rates to colors

Add BAMM-inferred rate shifts to a phylogeny plot

credibleShiftSet

Credible set of macroevolutionary rate shift configurations from BAMM results

Add a color legend to a phylo-rate plot

Calculate BAMM likelihood

computeBayesFactors

Compute Bayes Factors

Visualize macroevolutionary cohorts

getBestShiftConfiguration

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

getBranchShiftPriors

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

Jenks natural breaks classification

Create bammdata object from MCMC output

generateControlFile

Generate control file for BAMM

Compute clade-specific mean rates

Calculate macroevolutionary rate changes on a phylogeny from BAMM output

getMarginalBranchRateMatrix

Compute mean branch rates for bammdata object

getCohortMatrix

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

getMeanBranchLengthTree

Compute phylogeny with branch lengths equal to corresponding macroevolutionary rate estimates

maximumShiftCredibility

Estimate maximum shift credibility configuration

Compute tip-specific macroevolutionary rates from bammdata object

getRateThroughTimeMatrix

Generate rate-through-time matrix from bammdata object

Plot BAMM-estimated macroevolutionary rates on a phylogeny

plot.bammshifts

Plot distinct rate shift configurations on a phylogeny

Find most recent common ancestors

getShiftNodesFromIndex

Identify nodes associated with rate shifts from bammdata object

plot.credibleshiftset

Plot credible set of rate shift configurations from BAMM analysis

marginalOddsRatioBranches

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

Plot the prior and posterior distribution of shifts

plotRateThroughTime

Plot rates through time

Rich color palette

Set BAMM Priors

speciesByRatesMatrix

Compute species-specific rate through time trajectories

cumulativeShiftProbsTree

Branch-specific rate shift probabilities

Identify the optimal number of shifts using Bayes factors

Pulls out a subtree from bammdata object

subsetEventData

Subset a bammdata object

Creates clade-specific sampling fractions

Histogram of BAMM rate frequencies

Write a bammdata object to disk

summary.bammdata

Summary of rate shift results from BAMM analysis

traitDependentBAMM

STRAPP: STructured Rate Permutations on Phylogenies

testTimeVariableBranches

Evaluate evidence for temporal rate variation across tree

transparentColor

Define colors with transparency

summary.credibleshiftset

Summary of credible set of shift configurations from a BAMM analysis