BAMMlikelihood          Calculate 'BAMM' likelihood
BAMMtools               BAMMtools
BAMMtools-data          BAMMtools datasets
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
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
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
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
getmrca                 Find most recent common ancestors
marginalOddsRatioBranches
                        Ratio of (marginal) posterior-to-prior
                        probabilities on individual branches
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' analysis
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
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' analysis
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
