Files in BAMMtools
Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

inst
inst/CITATION
src
src/treetraverse.c
src/cohort_matrix.c
src/jenksBrks.c
src/dtrates.c
NAMESPACE
data
data/primates.rda
data/fishes.rda
data/events.primates.rda
data/events.fishes.rda
data/traits.fishes.rda
data/mcmc.whales.rda
data/mass.primates.rda
data/whales.rda
data/events.whales.rda
data/mcmc.primates.rda
R
R/distinctShiftConfigurations.R R/credibleShiftSet.R R/getShiftNodesFromIndex.R R/NU.branching.times.R R/speciesByRatesMatrix.R R/bammLikelihood.R R/barLegend.R R/getDesc.R R/getMarginalBranchRateMatrix.R R/subsetEventData.R R/logit.R R/areShiftSetsEqual.R R/writeEventData.R R/getTipRates.R R/setBAMMpriors.R R/plot.bammdata.R R/colorMap.R R/as.bammdata.R R/print.bammdata.R R/getJenksBreaks.R R/as.phylo.bammdata.R R/maximumShiftCredibility.R R/rateLegend.R R/plot.bammshifts.R R/mkdtsegsPhylo.R R/timeIntegratedBranchRate.R R/getStartStopTimes.R R/testTimeVariableBranches.R R/getRateThroughTimeMatrix.R R/setPolarTreeCoords.R R/traitDependentBAMM.R R/cohorts.R R/getRecursiveSequence.R R/transparentColor.R R/getBestShiftConfiguration.R R/subtreeBAMM.R R/getEventData.R R/arc.R R/plot.credibleshiftset.R R/assignColorBreaks.R R/branchMeanRateExponential.R R/marginalShiftProbsTree.R R/plotPrior.R R/getPathToRoot.R R/getmrca.R R/getBranchShiftPriors.R R/generateControlFile.R R/inv.logit.R R/segMap.R R/getMeanBranchLengthTree.R R/getCohortMatrix.R R/getSequenceForwardTraversal.R R/getSpanningTaxonPair.R R/exponentialRate.R R/addBAMMlegend.R R/mkdtsegsPolar.R R/setPhyloTreeCoords.R R/plotRateThroughTime.R R/bammcolors.R R/getCladeRates.R R/BAMMtools-data.R R/samplingProbs.R R/cumulativeShiftProbsTree.R R/ratesHistogram.R R/areEventConfigurationsIdentical.R R/marginalOddsRatioBranches.R R/BAMMtools-package.R R/stepBF.R R/summary.bammdata.R R/dtRates.R R/computeBayesFactors.R R/fxnDeps.R R/addBAMMshifts.R R/recursivelySetNodeStates.R R/summary.credibleshiftset.R R/phylogeneticMean.R
MD5
DESCRIPTION
man
man/getEventData.Rd man/getCladeRates.Rd man/summary.bammdata.Rd man/BAMMlikelihood.Rd man/subsetEventData.Rd man/getBestShiftConfiguration.Rd man/richColors.Rd man/addBAMMshifts.Rd man/computeBayesFactors.Rd man/getTipRates.Rd man/dtRates.Rd man/plotPrior.Rd man/addBAMMlegend.Rd man/generateControlFile.Rd man/cohorts.Rd man/distinctShiftConfigurations.Rd man/getRateThroughTimeMatrix.Rd man/setBAMMpriors.Rd man/getmrca.Rd man/BAMMtools-data.Rd man/getShiftNodesFromIndex.Rd man/credibleShiftSet.Rd man/getBranchShiftPriors.Rd man/testTimeVariableBranches.Rd man/plot.bammshifts.Rd man/getJenksBreaks.Rd man/speciesByRatesMatrix.Rd man/ratesHistogram.Rd man/BAMMtools.Rd man/transparentColor.Rd man/stepBF.Rd man/ShiftProbsTree.Rd man/plot.bammdata.Rd man/writeEventData.Rd man/getCohortMatrix.Rd man/maximumShiftCredibility.Rd man/plot.credibleshiftset.Rd man/subtreeBAMM.Rd man/plotRateThroughTime.Rd man/traitDependentBAMM.Rd man/getMarginalBranchRateMatrix.Rd man/marginalOddsRatioBranches.Rd man/summary.credibleshiftset.Rd man/getMeanBranchLengthTree.Rd man/assignColorBreaks.Rd man/samplingProbs.Rd
BAMMtools documentation built on May 29, 2017, 5:47 p.m.