BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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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.

Author
Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Date of publication
2016-10-03 22:47:14
Maintainer
Pascal Title <ptitle@umich.edu>
License
GPL (>= 2)
Version
2.1.5
URLs

View on CRAN

Man pages

addBAMMlegend
Add a color legend to a phylo-rate plot
addBAMMshifts
Add 'BAMM'-inferred rate shifts to a phylogeny plot
assignColorBreaks
Map macroevolutionary rates to colors
BAMMlikelihood
Calculate 'BAMM' likelihood
BAMMtools
BAMMtools
BAMMtools-data
BAMMtools datasets
cohorts
Visualize macroevolutionary cohorts
computeBayesFactors
Compute Bayes Factors
credibleShiftSet
Credible set of macroevolutionary rate shift configurations...
distinctShiftConfigurations
Identify distinct rate shift configurations
dtRates
Calculate macroevolutionary rate changes on a phylogeny from...
generateControlFile
Generate control file for 'BAMM'
getBestShiftConfiguration
Get the best (sampled) rate shift configuration from a 'BAMM'...
getBranchShiftPriors
Compute prior odds of a rate shift on each branch of a...
getCladeRates
Compute clade-specific mean rates
getCohortMatrix
Compute the pairwise correlation in rate regimes between all...
getEventData
Create 'bammdata' object from MCMC output
getJenksBreaks
Jenks natural breaks classification
getMarginalBranchRateMatrix
Compute mean branch rates for 'bammdata' object
getMeanBranchLengthTree
Compute phylogeny with branch lengths equal to corresponding...
getmrca
Find most recent common ancestors
getRateThroughTimeMatrix
Generate rate-through-time matrix from 'bammdata' object
getShiftNodesFromIndex
Identify nodes associated with rate shifts from 'bammdata'...
getTipRates
Compute tip-specific macroevolutionary rates from 'bammdata'...
marginalOddsRatioBranches
Ratio of (marginal) posterior-to-prior probabilities on...
maximumShiftCredibility
Estimate maximum shift credibility configuration
plot.bammdata
Plot 'BAMM'-estimated macroevolutionary rates on a phylogeny
plot.bammshifts
Plot distinct rate shift configurations on a phylogeny
plot.credibleshiftset
Plot credible set of rate shift configurations from 'BAMM'...
plotPrior
Plot the prior and posterior distribution of shifts
plotRateThroughTime
Plot rates through time
ratesHistogram
Histogram of 'BAMM' rate frequencies
richColors
Rich color palette
samplingProbs
Creates clade-specific sampling fractions
setBAMMpriors
Set BAMM Priors
ShiftProbsTree
Branch-specific rate shift probabilities
speciesByRatesMatrix
Compute species-specific rate through time trajectories
stepBF
Identify the optimal number of shifts using Bayes factors
subsetEventData
Subset a 'bammdata' object
subtreeBAMM
Pulls out a subtree from 'bammdata' object
summary.bammdata
Summary of rate shift results from 'BAMM' analysis
summary.credibleshiftset
Summary of credible set of shift configurations from a 'BAMM'...
testTimeVariableBranches
Evaluate evidence for temporal rate variation across tree
traitDependentBAMM
STRAPP: STructured Rate Permutations on Phylogenies
transparentColor
Define colors with transparency
writeEventData
Write a 'bammdata' object to disk

Files in this package

BAMMtools
BAMMtools/inst
BAMMtools/inst/CITATION
BAMMtools/src
BAMMtools/src/treetraverse.c
BAMMtools/src/cohort_matrix.c
BAMMtools/src/jenksBrks.c
BAMMtools/src/dtrates.c
BAMMtools/NAMESPACE
BAMMtools/data
BAMMtools/data/primates.rda
BAMMtools/data/fishes.rda
BAMMtools/data/events.primates.rda
BAMMtools/data/events.fishes.rda
BAMMtools/data/traits.fishes.rda
BAMMtools/data/mcmc.whales.rda
BAMMtools/data/mass.primates.rda
BAMMtools/data/whales.rda
BAMMtools/data/events.whales.rda
BAMMtools/data/mcmc.primates.rda
BAMMtools/R
BAMMtools/R/distinctShiftConfigurations.R
BAMMtools/R/credibleShiftSet.R
BAMMtools/R/getShiftNodesFromIndex.R
BAMMtools/R/NU.branching.times.R
BAMMtools/R/speciesByRatesMatrix.R
BAMMtools/R/bammLikelihood.R
BAMMtools/R/barLegend.R
BAMMtools/R/getDesc.R
BAMMtools/R/getMarginalBranchRateMatrix.R
BAMMtools/R/subsetEventData.R
BAMMtools/R/logit.R
BAMMtools/R/areShiftSetsEqual.R
BAMMtools/R/writeEventData.R
BAMMtools/R/getTipRates.R
BAMMtools/R/setBAMMpriors.R
BAMMtools/R/plot.bammdata.R
BAMMtools/R/colorMap.R
BAMMtools/R/as.bammdata.R
BAMMtools/R/print.bammdata.R
BAMMtools/R/getJenksBreaks.R
BAMMtools/R/as.phylo.bammdata.R
BAMMtools/R/maximumShiftCredibility.R
BAMMtools/R/rateLegend.R
BAMMtools/R/plot.bammshifts.R
BAMMtools/R/mkdtsegsPhylo.R
BAMMtools/R/timeIntegratedBranchRate.R
BAMMtools/R/getStartStopTimes.R
BAMMtools/R/testTimeVariableBranches.R
BAMMtools/R/getRateThroughTimeMatrix.R
BAMMtools/R/setPolarTreeCoords.R
BAMMtools/R/traitDependentBAMM.R
BAMMtools/R/cohorts.R
BAMMtools/R/getRecursiveSequence.R
BAMMtools/R/transparentColor.R
BAMMtools/R/getBestShiftConfiguration.R
BAMMtools/R/subtreeBAMM.R
BAMMtools/R/getEventData.R
BAMMtools/R/arc.R
BAMMtools/R/plot.credibleshiftset.R
BAMMtools/R/assignColorBreaks.R
BAMMtools/R/branchMeanRateExponential.R
BAMMtools/R/marginalShiftProbsTree.R
BAMMtools/R/plotPrior.R
BAMMtools/R/getPathToRoot.R
BAMMtools/R/getmrca.R
BAMMtools/R/getBranchShiftPriors.R
BAMMtools/R/generateControlFile.R
BAMMtools/R/inv.logit.R
BAMMtools/R/segMap.R
BAMMtools/R/getMeanBranchLengthTree.R
BAMMtools/R/getCohortMatrix.R
BAMMtools/R/getSequenceForwardTraversal.R
BAMMtools/R/getSpanningTaxonPair.R
BAMMtools/R/exponentialRate.R
BAMMtools/R/addBAMMlegend.R
BAMMtools/R/mkdtsegsPolar.R
BAMMtools/R/setPhyloTreeCoords.R
BAMMtools/R/plotRateThroughTime.R
BAMMtools/R/bammcolors.R
BAMMtools/R/getCladeRates.R
BAMMtools/R/BAMMtools-data.R
BAMMtools/R/samplingProbs.R
BAMMtools/R/cumulativeShiftProbsTree.R
BAMMtools/R/ratesHistogram.R
BAMMtools/R/areEventConfigurationsIdentical.R
BAMMtools/R/marginalOddsRatioBranches.R
BAMMtools/R/BAMMtools-package.R
BAMMtools/R/stepBF.R
BAMMtools/R/summary.bammdata.R
BAMMtools/R/dtRates.R
BAMMtools/R/computeBayesFactors.R
BAMMtools/R/fxnDeps.R
BAMMtools/R/addBAMMshifts.R
BAMMtools/R/recursivelySetNodeStates.R
BAMMtools/R/summary.credibleshiftset.R
BAMMtools/R/phylogeneticMean.R
BAMMtools/MD5
BAMMtools/DESCRIPTION
BAMMtools/man
BAMMtools/man/getEventData.Rd
BAMMtools/man/getCladeRates.Rd
BAMMtools/man/summary.bammdata.Rd
BAMMtools/man/BAMMlikelihood.Rd
BAMMtools/man/subsetEventData.Rd
BAMMtools/man/getBestShiftConfiguration.Rd
BAMMtools/man/richColors.Rd
BAMMtools/man/addBAMMshifts.Rd
BAMMtools/man/computeBayesFactors.Rd
BAMMtools/man/getTipRates.Rd
BAMMtools/man/dtRates.Rd
BAMMtools/man/plotPrior.Rd
BAMMtools/man/addBAMMlegend.Rd
BAMMtools/man/generateControlFile.Rd
BAMMtools/man/cohorts.Rd
BAMMtools/man/distinctShiftConfigurations.Rd
BAMMtools/man/getRateThroughTimeMatrix.Rd
BAMMtools/man/setBAMMpriors.Rd
BAMMtools/man/getmrca.Rd
BAMMtools/man/BAMMtools-data.Rd
BAMMtools/man/getShiftNodesFromIndex.Rd
BAMMtools/man/credibleShiftSet.Rd
BAMMtools/man/getBranchShiftPriors.Rd
BAMMtools/man/testTimeVariableBranches.Rd
BAMMtools/man/plot.bammshifts.Rd
BAMMtools/man/getJenksBreaks.Rd
BAMMtools/man/speciesByRatesMatrix.Rd
BAMMtools/man/ratesHistogram.Rd
BAMMtools/man/BAMMtools.Rd
BAMMtools/man/transparentColor.Rd
BAMMtools/man/stepBF.Rd
BAMMtools/man/ShiftProbsTree.Rd
BAMMtools/man/plot.bammdata.Rd
BAMMtools/man/writeEventData.Rd
BAMMtools/man/getCohortMatrix.Rd
BAMMtools/man/maximumShiftCredibility.Rd
BAMMtools/man/plot.credibleshiftset.Rd
BAMMtools/man/subtreeBAMM.Rd
BAMMtools/man/plotRateThroughTime.Rd
BAMMtools/man/traitDependentBAMM.Rd
BAMMtools/man/getMarginalBranchRateMatrix.Rd
BAMMtools/man/marginalOddsRatioBranches.Rd
BAMMtools/man/summary.credibleshiftset.Rd
BAMMtools/man/getMeanBranchLengthTree.Rd
BAMMtools/man/assignColorBreaks.Rd
BAMMtools/man/samplingProbs.Rd