API for BAMMtools
Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

Global functions
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 Source code
eventMatrix Source code
events.fishes Man page
events.primates Man page
events.whales Man page
exponentialRate Source code
fishes Man page
fxnDeps Source code
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
inv.logit Source code
logit 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 Source code
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 Source code
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
BAMMtools documentation built on May 29, 2017, 5:47 p.m.