BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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.

AuthorDan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Date of publication2017-02-03 08:13:22
MaintainerPascal Title <ptitle@umich.edu>
LicenseGPL (>= 2)
Version2.1.6
http://www.bamm-project.org

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

Functions

addBAMMlegend Man page
addBAMMshifts Man page
assignColorBreaks Man page
BAMMlikelihood Man page
BAMMtools Man page
BAMMtools-data Man page
BAMMtools-package Man page
cohorts Man page
computeBayesFactors Man page
credibleShiftSet Man page
cumulativeShiftProbsTree Man page
distinctShiftConfigurations Man page
dtRates Man page
events.fishes Man page
events.primates Man page
events.whales Man page
fishes Man page
generateControlFile Man page
getBestShiftConfiguration Man page
getBranchShiftPriors Man page
getCladeRates Man page
getCohortMatrix Man page
getEventData Man page
getJenksBreaks Man page
getMarginalBranchRateMatrix Man page
getMeanBranchLengthTree Man page
getmrca Man page
getRateThroughTimeMatrix Man page
getShiftNodesFromIndex Man page
getTipRates Man page
marginalOddsRatioBranches Man page
marginalShiftProbsTree Man page
mass.primates Man page
maximumShiftCredibility Man page
mcmc.primates Man page
mcmc.whales Man page
plot.bammdata Man page
plot.bammshifts Man page
plot.credibleshiftset Man page
plotPrior Man page
plotRateThroughTime Man page
primates Man page
print.credibleshiftset Man page
ratesHistogram Man page
richColors Man page
samplingProbs Man page
setBAMMpriors Man page
speciesByRatesMatrix Man page
stepBF Man page
strapp Man page
subsetEventData Man page
subtreeBAMM Man page
summary.bammdata Man page
summary.credibleshiftset Man page
testTimeVariableBranches Man page
traitDependentBAMM Man page
traits.fishes Man page
transparentColor Man page
whales Man page
writeEventData Man page

Files

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

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