Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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Documentation for package ‘BAMMtools’ version 2.1.11

• DESCRIPTION file.

Help 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 from 'BAMM' results
cumulativeShiftProbsTree	Branch-specific rate shift probabilities
distinctShiftConfigurations	Identify distinct rate shift configurations
dtRates	Calculate macroevolutionary rate changes on a phylogeny from 'BAMM' output
events.fishes	BAMMtools datasets
events.primates	BAMMtools datasets
events.whales	BAMMtools datasets
fishes	BAMMtools datasets
generateControlFile	Generate control file for 'BAMM'
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
getCladeRates	Compute clade-specific mean rates
getCohortMatrix	Compute the pairwise correlation in rate regimes between all tips in a 'bammdata' object
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 macroevolutionary rate estimates
getmrca	Find most recent common ancestors
getRateThroughTimeMatrix	Generate rate-through-time matrix from 'bammdata' object
getShiftNodesFromIndex	Identify nodes associated with rate shifts from 'bammdata' object
getTipRates	Compute tip-specific macroevolutionary rates from 'bammdata' object
marginalOddsRatioBranches	Ratio of (marginal) posterior-to-prior probabilities on individual branches
marginalShiftProbsTree	Branch-specific rate shift probabilities
mass.primates	BAMMtools datasets
maximumShiftCredibility	Estimate maximum shift credibility configuration
mcmc.primates	BAMMtools datasets
mcmc.whales	BAMMtools datasets
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' analysis
plotPrior	Plot the prior and posterior distribution of shifts
plotRateThroughTime	Plot rates through time
primates	BAMMtools datasets
print.credibleshiftset	Summary of credible set of shift configurations from a 'BAMM' analysis
ratesHistogram	Histogram of 'BAMM' rate frequencies
richColors	Rich color palette
samplingProbs	Creates clade-specific sampling fractions
setBAMMpriors	Set BAMM Priors
speciesByRatesMatrix	Compute species-specific rate through time trajectories
stepBF	Identify the optimal number of shifts using Bayes factors
strapp	STRAPP: STructured Rate Permutations on Phylogenies
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' analysis
testTimeVariableBranches	Evaluate evidence for temporal rate variation across tree
traitDependentBAMM	STRAPP: STructured Rate Permutations on Phylogenies
traits.fishes	BAMMtools datasets
transparentColor	Define colors with transparency
whales	BAMMtools datasets
writeEventData	Write a 'bammdata' object to disk