BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
Version 2.1.6

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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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
URL http://www.bamm-project.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BAMMtools")

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

BAMMlikelihood Man page Source code
BAMMtools Man page
BAMMtools-data Man page
BAMMtools-package Man page
D_func Source code
E_func Source code
NU.branching.times Source code
addBAMMlegend Man page Source code
addBAMMshifts Man page Source code
arc Source code
areEventConfigurationsIdentical Source code
areShiftSetsEqual Source code
as.bammdata Source code
as.bammdata.credibleshiftset Source code
as.phylo.bammdata Source code
assignColorBreaks Man page Source code
barLegend Source code
branchMeanRateExponential Source code
buildSegmentMatricesRecursive Source code
buildSegmentMatrix Source code
buildTreeWithEventList Source code
cohorts Man page Source code
colorMap Source code
computeBAMMlikelihood Source code
computeBayesFactors Man page Source code
credibleShiftSet Man page Source code
cumulativeShiftProbsTree Man page Source code
distinctShiftConfigurations Man page Source code
dtRates Man page Source code
eventMatrix Source code
events.fishes Man page
events.primates Man page
events.whales Man page
exponentialRate Source code
fishes Man page
fxnDeps Source code
generateControlFile Man page Source code
getBestShiftConfiguration Man page Source code
getBranchShiftPriors Man page Source code
getCladeRates Man page Source code
getCohortMatrix Man page Source code
getDesc Source code
getEventData Man page Source code
getJenksBreaks Man page Source code
getMarginalBranchRateMatrix Man page Source code
getMeanBranchLengthTree Man page Source code
getPathToRoot Source code
getRateThroughTimeMatrix Man page Source code
getRecursiveSequence Source code
getSequenceForwardTraversal Source code
getShiftNodesFromIndex Man page Source code
getSpanningTaxonPair Source code
getStartStopTimes Source code
getTipRates Man page Source code
getmrca Man page Source code
inv.logit Source code
logit Source code
makeBDeventMatrix Source code
marginalOddsRatioBranches Man page Source code
marginalShiftProbsTree Man page Source code
mass.primates Man page
maximumShiftCredibility Man page Source code
mcmc.primates Man page
mcmc.whales Man page
meanExponentialRate Source code
mkdtsegsPhylo Source code
mkdtsegsPolar Source code
optimize1shiftBAMM Source code
phylogeneticMean Source code
plot.bammdata Man page Source code
plot.bammshifts Man page Source code
plot.credibleshiftset Man page Source code
plotPrior Man page Source code
plotRateThroughTime Man page Source code
primates Man page
print.bammdata Source code
print.credibleshiftset Man page Source code
prob.k Source code
rateLegend Source code
ratesHistogram Man page Source code
recursiveAddEventsToTree Source code
recursivelySetNodeStates Source code
redirect Source code
richColors Man page Source code
safeLog Source code
samplingProbs Man page Source code
segMap Source code
setBAMMpriors Man page Source code
setPhyloTreeCoords Source code
setPolarTreeCoords Source code
speciesByRatesMatrix Man page Source code
stepBF Man page Source code
strapp Man page
subsetEventData Man page Source code
subtreeBAMM Man page Source code
summary.bammdata Man page Source code
summary.credibleshiftset Man page Source code
testTimeVariableBranches Man page Source code
timeIntegratedBranchRate Source code
traitDependentBAMM Man page Source code
traits.fishes Man page
transparentColor Man page Source code
whales Man page
writeEventData Man page Source code

Files

inst
inst/CITATION
src
src/treetraverse.c
src/cohort_matrix.c
src/jenksBrks.c
src/dtrates.c
NAMESPACE
data
data/primates.rda
data/fishes.rda
data/events.primates.rda
data/events.fishes.rda
data/traits.fishes.rda
data/mcmc.whales.rda
data/mass.primates.rda
data/whales.rda
data/events.whales.rda
data/mcmc.primates.rda
R
R/distinctShiftConfigurations.R
R/credibleShiftSet.R
R/getShiftNodesFromIndex.R
R/NU.branching.times.R
R/speciesByRatesMatrix.R
R/bammLikelihood.R
R/barLegend.R
R/getDesc.R
R/getMarginalBranchRateMatrix.R
R/subsetEventData.R
R/logit.R
R/areShiftSetsEqual.R
R/writeEventData.R
R/getTipRates.R
R/setBAMMpriors.R
R/plot.bammdata.R
R/colorMap.R
R/as.bammdata.R
R/print.bammdata.R
R/getJenksBreaks.R
R/as.phylo.bammdata.R
R/maximumShiftCredibility.R
R/rateLegend.R
R/plot.bammshifts.R
R/mkdtsegsPhylo.R
R/timeIntegratedBranchRate.R
R/getStartStopTimes.R
R/testTimeVariableBranches.R
R/getRateThroughTimeMatrix.R
R/setPolarTreeCoords.R
R/traitDependentBAMM.R
R/cohorts.R
R/getRecursiveSequence.R
R/transparentColor.R
R/getBestShiftConfiguration.R
R/subtreeBAMM.R
R/getEventData.R
R/arc.R
R/plot.credibleshiftset.R
R/assignColorBreaks.R
R/branchMeanRateExponential.R
R/marginalShiftProbsTree.R
R/plotPrior.R
R/getPathToRoot.R
R/getmrca.R
R/getBranchShiftPriors.R
R/generateControlFile.R
R/inv.logit.R
R/segMap.R
R/getMeanBranchLengthTree.R
R/getCohortMatrix.R
R/getSequenceForwardTraversal.R
R/getSpanningTaxonPair.R
R/exponentialRate.R
R/addBAMMlegend.R
R/mkdtsegsPolar.R
R/setPhyloTreeCoords.R
R/plotRateThroughTime.R
R/bammcolors.R
R/getCladeRates.R
R/BAMMtools-data.R
R/samplingProbs.R
R/cumulativeShiftProbsTree.R
R/ratesHistogram.R
R/areEventConfigurationsIdentical.R
R/marginalOddsRatioBranches.R
R/BAMMtools-package.R
R/stepBF.R
R/summary.bammdata.R
R/dtRates.R
R/computeBayesFactors.R
R/fxnDeps.R
R/addBAMMshifts.R
R/recursivelySetNodeStates.R
R/summary.credibleshiftset.R
R/phylogeneticMean.R
MD5
DESCRIPTION
man
man/getEventData.Rd
man/getCladeRates.Rd
man/summary.bammdata.Rd
man/BAMMlikelihood.Rd
man/subsetEventData.Rd
man/getBestShiftConfiguration.Rd
man/richColors.Rd
man/addBAMMshifts.Rd
man/computeBayesFactors.Rd
man/getTipRates.Rd
man/dtRates.Rd
man/plotPrior.Rd
man/addBAMMlegend.Rd
man/generateControlFile.Rd
man/cohorts.Rd
man/distinctShiftConfigurations.Rd
man/getRateThroughTimeMatrix.Rd
man/setBAMMpriors.Rd
man/getmrca.Rd
man/BAMMtools-data.Rd
man/getShiftNodesFromIndex.Rd
man/credibleShiftSet.Rd
man/getBranchShiftPriors.Rd
man/testTimeVariableBranches.Rd
man/plot.bammshifts.Rd
man/getJenksBreaks.Rd
man/speciesByRatesMatrix.Rd
man/ratesHistogram.Rd
man/BAMMtools.Rd
man/transparentColor.Rd
man/stepBF.Rd
man/ShiftProbsTree.Rd
man/plot.bammdata.Rd
man/writeEventData.Rd
man/getCohortMatrix.Rd
man/maximumShiftCredibility.Rd
man/plot.credibleshiftset.Rd
man/subtreeBAMM.Rd
man/plotRateThroughTime.Rd
man/traitDependentBAMM.Rd
man/getMarginalBranchRateMatrix.Rd
man/marginalOddsRatioBranches.Rd
man/summary.credibleshiftset.Rd
man/getMeanBranchLengthTree.Rd
man/assignColorBreaks.Rd
man/samplingProbs.Rd
BAMMtools documentation built on May 19, 2017, 3:35 p.m.