API for BAMMtools
Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
| Global functions | |
|---|---|
| .fxnDeps | Source code |
| BAMMlikelihood | Man page Source code |
| BAMMtools | Man page |
| BAMMtools-data | Man page |
| BAMMtools-package | Man page |
| D_func | Source code |
| E_func | Source code |
| NU.branching.times | Source code |
| addBAMMlegend | Man page Source code |
| addBAMMshifts | Man page Source code |
| arc | Source code |
| areEventConfigurationsIdentical | Source code |
| areShiftSetsEqual | Source code |
| as.bammdata | Source code |
| as.bammdata.credibleshiftset | Source code |
| as.phylo.bammdata | Source code |
| assignColorBreaks | Man page Source code |
| barLegend | Source code |
| branchMeanRateExponential | Source code |
| buildSegmentMatricesRecursive | Source code |
| buildSegmentMatrix | Source code |
| buildTreeWithEventList | Source code |
| cohorts | Man page Source code |
| colorMap | Source code |
| computeBAMMlikelihood | Source code |
| computeBayesFactors | Man page Source code |
| credibleShiftSet | Man page Source code |
| cumulativeShiftProbsTree | Man page Source code |
| distinctShiftConfigurations | Man page Source code |
| dtRates | Man page |
| eventMatrix | Source code |
| events.fishes | Man page |
| events.primates | Man page |
| events.whales | Man page |
| exponentialRate | Source code |
| fishes | Man page |
| generateControlFile | Man page Source code |
| getBestShiftConfiguration | Man page Source code |
| getBranchShiftPriors | Man page Source code |
| getCladeRates | Man page Source code |
| getCohortMatrix | Man page Source code |
| getDesc | Source code |
| getEventData | Man page Source code |
| getJenksBreaks | Man page Source code |
| getMarginalBranchRateMatrix | Man page Source code |
| getMeanBranchLengthTree | Man page Source code |
| getPathToRoot | Source code |
| getRateThroughTimeMatrix | Man page Source code |
| getRecursiveSequence | Source code |
| getSequenceForwardTraversal | Source code |
| getShiftNodesFromIndex | Man page Source code |
| getSpanningTaxonPair | Source code |
| getStartStopTimes | Source code |
| getTipRates | Man page Source code |
| getmrca | Man page Source code |
| makeBDeventMatrix | Source code |
| marginalOddsRatioBranches | Man page Source code |
| marginalShiftProbsTree | Man page Source code |
| mass.primates | Man page |
| maximumShiftCredibility | Man page Source code |
| mcmc.primates | Man page |
| mcmc.whales | Man page |
| meanExponentialRate | Source code |
| mkdtsegsPhylo | Source code |
| mkdtsegsPolar | Source code |
| optimize1shiftBAMM | Source code |
| phylogeneticMean | Source code |
| plot.bammdata | Man page |
| plot.bammshifts | Man page Source code |
| plot.credibleshiftset | Man page Source code |
| plotPrior | Man page Source code |
| plotRateThroughTime | Man page Source code |
| primates | Man page |
| print.bammdata | Source code |
| print.credibleshiftset | Man page Source code |
| prob.k | Source code |
| rateLegend | Source code |
| ratesHistogram | Man page Source code |
| recursiveAddEventsToTree | Source code |
| recursivelySetNodeStates | Source code |
| redirect | Source code |
| richColors | Man page |
| safeLog | Source code |
| samplingProbs | Man page Source code |
| segMap | Source code |
| setBAMMpriors | Man page Source code |
| setPhyloTreeCoords | Source code |
| setPolarTreeCoords | Source code |
| speciesByRatesMatrix | Man page Source code |
| stepBF | Man page Source code |
| strapp | Man page |
| subsetEventData | Man page Source code |
| subtreeBAMM | Man page Source code |
| summary.bammdata | Man page Source code |
| summary.credibleshiftset | Man page Source code |
| testTimeVariableBranches | Man page Source code |
| timeIntegratedBranchRate | Source code |
| traitDependentBAMM | Man page Source code |
| traits.fishes | Man page |
| transparentColor | Man page Source code |
| whales | Man page |
| writeEventData | Man page Source code |
