# Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

## Documentation for package ‘BAMMtools’ version 2.1.12

- DESCRIPTION file.

## Help Pages

BAMMtools-package | BAMMtools
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