Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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Documentation for package ‘BAMMtools’ version 2.1.7

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