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| BAMMtools-package | BAMMtools |
| addBAMMlegend | Add a color legend to a phylo-rate plot |
| addBAMMshifts | Add BAMM-inferred rate shifts to a phylogeny plot |
| arc | Internal BAMMtools functions |
| areEventConfigurationsIdentical | Internal BAMMtools functions |
| areShiftSetsEqual | Internal BAMMtools functions |
| as.bammdata | Internal BAMMtools functions |
| as.bammdata.credibleshiftset | Internal BAMMtools functions |
| as.phylo.bammdata | Internal BAMMtools functions |
| as.phylo.branchprior | Internal BAMMtools functions |
| assignColorBreaks | Map macroevolutionary rates to colors |
| BAMMtools | BAMMtools |
| barLegend | Internal BAMMtools functions |
| bayesFactorBranches | Bayes factor evidence for rate shifts on individual branches |
| branchMeanRateExponential | Internal BAMMtools functions |
| cohorts | Visualize macroevolutionary cohorts |
| colorMap | Internal BAMMtools functions |
| computeBayesFactors | computeBayesFactors |
| 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 |
| exponentialRate | Internal BAMMtools functions |
| fishes | BAMMtools datasets |
| getBAMMCorrelationMatrix | Compute the pairwise correlation in rate regimes between all tips in a bammdata object |
| 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 |
| getDesc | Internal BAMMtools functions |
| getEventData | Create 'bammdata' object from MCMC output |
| getJenksBreaks | Jenks natural breaks classification |
| getMacroevolutionaryCohortMatrix | Compute the pairwise correlation in rate regimes between all tips in a bammdata object |
| 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 |
| getPathToRoot | Internal BAMMtools functions |
| getRateThroughTimeMatrix | Generate rate-through-time matrix from 'bammdata' object |
| getRecursiveSequence | Internal BAMMtools functions |
| getSampleCoMat | Internal BAMMtools functions |
| getSequenceForwardTraversal | Internal BAMMtools functions |
| getShiftNodesFromIndex | Identify nodes associated with rate shifts from 'bammdata' object |
| getSpanningTaxonPair | Internal BAMMtools functions |
| getStartStopTimes | Internal BAMMtools functions |
| getTipRates | Compute tip-specific macroevolutionary rates from 'bammdata' object |
| inv.logit | Internal BAMMtools functions |
| logit | Internal BAMMtools functions |
| marginalShiftProbsTree | Branch-specific rate shift probabilities |
| mass.primates | BAMMtools datasets |
| maximumShiftCredibility | Estimate maximum shift credibility configuration |
| mcmc.primates | BAMMtools datasets |
| mcmc.whales | BAMMtools datasets |
| mkdtsegsPhylo | Internal BAMMtools functions |
| mkdtsegsPolar | Internal BAMMtools functions |
| NU.branching.times | Internal BAMMtools functions |
| palettes | Internal BAMMtools functions |
| phylogeneticMean | Internal BAMMtools functions |
| 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 |
| plotRateThroughTime | Plot rates through time |
| primates | BAMMtools datasets |
| print.bammdata | Internal BAMMtools functions |
| print.branchprior | Summary of class "branchprior" object. |
| print.credibleshiftset | Summary of credible set of shift configurations from a 'BAMM' analysis. |
| prior.primates | BAMMtools datasets |
| prior.whales | BAMMtools datasets |
| rateLegend | Internal BAMMtools functions |
| recursivelySetNodeStates | Internal BAMMtools functions |
| redirect | Internal BAMMtools functions |
| richColors | Internal BAMMtools functions |
| safeLog | Internal BAMMtools functions |
| samplingProbs | Creates clade-specific sampling fractions |
| segMap | Internal BAMMtools functions |
| setBAMMpriors | setBAMMpriors |
| setPhyloTreeCoords | Internal BAMMtools functions |
| setPolarTreeCoords | Internal BAMMtools functions |
| speciesByRatesMatrix | Compute species-specific rate through time trajectories |
| subsetEventData | Subset a 'bammdata' object |
| subtreeBAMM | Pulls out a subtree from bammdata object |
| summary.bammdata | Summary of rate shift results from 'BAMM' analysis. |
| summary.branchprior | Summary of class "branchprior" object. |
| summary.credibleshiftset | Summary of credible set of shift configurations from a 'BAMM' analysis. |
| testTimeVariableBranches | Evaluate evidence for temporal rate variation across tree |
| timeIntegratedBranchRate | Internal BAMMtools functions |
| traitDependentBAMM | STRAPP: STructured Rate Permutations on Phylogenies |
| traits.fishes | BAMMtools datasets |
| transparentColor | Internal BAMMtools functions |
| whales | BAMMtools datasets |
| writeEventData | Write a 'bammdata' object to disk |