Man pages for BAMMtools
Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

addBAMMlegendAdd a color legend to a phylo-rate plot
addBAMMshiftsAdd 'BAMM'-inferred rate shifts to a phylogeny plot
assignColorBreaksMap macroevolutionary rates to colors
BAMMlikelihoodCalculate 'BAMM' likelihood
BAMMtoolsBAMMtools
BAMMtools-dataBAMMtools datasets
cohortsVisualize macroevolutionary cohorts
computeBayesFactorsCompute Bayes Factors
credibleShiftSetCredible set of macroevolutionary rate shift configurations...
distinctShiftConfigurationsIdentify distinct rate shift configurations
dtRatesCalculate macroevolutionary rate changes on a phylogeny from...
generateControlFileGenerate control file for 'BAMM'
getBestShiftConfigurationGet the best (sampled) rate shift configuration from a 'BAMM'...
getBranchShiftPriorsCompute prior odds of a rate shift on each branch of a...
getCladeRatesCompute clade-specific mean rates
getCohortMatrixCompute the pairwise correlation in rate regimes between all...
getEventDataCreate 'bammdata' object from MCMC output
getJenksBreaksJenks natural breaks classification
getMarginalBranchRateMatrixCompute mean branch rates for 'bammdata' object
getMeanBranchLengthTreeCompute phylogeny with branch lengths equal to corresponding...
getmrcaFind most recent common ancestors
getRateThroughTimeMatrixGenerate rate-through-time matrix from 'bammdata' object
getShiftNodesFromIndexIdentify nodes associated with rate shifts from 'bammdata'...
getTipRatesCompute tip-specific macroevolutionary rates from 'bammdata'...
marginalOddsRatioBranchesRatio of (marginal) posterior-to-prior probabilities on...
maximumShiftCredibilityEstimate maximum shift credibility configuration
plot.bammdataPlot 'BAMM'-estimated macroevolutionary rates on a phylogeny
plot.bammshiftsPlot distinct rate shift configurations on a phylogeny
plot.credibleshiftsetPlot credible set of rate shift configurations from 'BAMM'...
plotPriorPlot the prior and posterior distribution of shifts
plotRateThroughTimePlot rates through time
ratesHistogramHistogram of 'BAMM' rate frequencies
richColorsRich color palette
samplingProbsCreates clade-specific sampling fractions
setBAMMpriorsSet BAMM Priors
ShiftProbsTreeBranch-specific rate shift probabilities
speciesByRatesMatrixCompute species-specific rate through time trajectories
stepBFIdentify the optimal number of shifts using Bayes factors
subsetEventDataSubset a 'bammdata' object
subtreeBAMMPulls out a subtree from 'bammdata' object
summary.bammdataSummary of rate shift results from 'BAMM' analysis
summary.credibleshiftsetSummary of credible set of shift configurations from a 'BAMM'...
testTimeVariableBranchesEvaluate evidence for temporal rate variation across tree
traitDependentBAMMSTRAPP: STructured Rate Permutations on Phylogenies
transparentColorDefine colors with transparency
writeEventDataWrite a 'bammdata' object to disk
BAMMtools documentation built on May 29, 2017, 5:47 p.m.