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Model Objects
AbstractDiscreteTaxonData
AbstractHomologousDiscreteCharacterData
AverageDistanceMatrix
Bool
BranchLengthTree
CharacterHistoryRateModifier
CladogeneticProbabilityMatrix
CladogeneticSpeciationRateMatrix
ContinuousCharacterData
DistanceMatrix
Integer
IntegerPos
MatrixBoolean
MatrixReal
MatrixRealPos
MatrixRealSymmetric
Natural
Probability
RateGenerator
Real
RealPos
RlRegionalFeatureLayer
Simplex
StochasticMatrix
String
TimeTree
Tree
clade
taxon
Distributions
dnBernoulli
dnBeta
dnBimodalLognormal
dnBimodalNormal
dnBinomial
dnBirthDeath
dnBirthDeathBurstProcess
dnBirthDeathSamplingTreatment
dnBivariatePoisson
dnBranchRateTree
dnCBDSP
dnCDBDP
dnCTMC
dnCategorical
dnCauchy
dnChisq
dnCoalescent
dnCoalescentDemography
dnCoalescentSkyline
dnCompleteBirthDeath
dnConstrainedNodeAge
dnConstrainedNodeOrder
dnConstrainedTopology
dnCppNormal
dnDPP
dnDecomposedInvWishart
dnDirichlet
dnDiversityDependentYule
dnDuplicationLoss
dnEmpiricalSample
dnEmpiricalTree
dnEpisodicBirthDeath
dnEvent
dnExponential
dnExponentialError
dnFossilizedBirthDeath
dnFossilizedBirthDeathRange
dnFossilizedBirthDeathSpecies
dnGamma
dnGeneralizedLineageHeterogeneousBirthDeathProcess
dnGeometric
dnGilbertGraph
dnHBDP
dnHalfCauchy
dnHalfNormal
dnHeterochronousCoalescent
dnHeterochronousCoalescentSkyline
dnIID
dnInverseGamma
dnInverseWishart
dnLKJ
dnLKJPartial
dnLaplace
dnLogExponential
dnLognormal
dnLoguniform
dnMarkovEvents
dnMarkovTimes
dnMixture
dnMixtureAnalytical
dnMixtureVector
dnMultiSpeciesCoalescent
dnMultiSpeciesCoalescentInverseGamma
dnMultiSpeciesCoalescentUniformPrior
dnMultiValueEvent
dnMultinomial
dnMultispeciesCoalescentMigration
dnMultivariateNormal
dnNbinomial
dnNormal
dnOrnsteinUhlenbeck
dnOutgroupBirthDeath
dnPhyloBranchRateBM
dnPhyloBrownian
dnPhyloBrownianMVN
dnPhyloBrownianMultiSampleREML
dnPhyloBrownianMultiVariate
dnPhyloBrownianREML
dnPhyloCTMC
dnPhyloCTMCClado
dnPhyloCTMCDASequence
dnPhyloCTMCDASiteIID
dnPhyloCTMCDollo
dnPhyloDistanceGamma
dnPhyloMultiSampleOrnsteinUhlenbeck
dnPhyloMultiSampleOrnsteinUhlenbeckREML
dnPhyloMultivariateBrownianMultiSampleREML
dnPhyloMultivariateBrownianREML
dnPhyloOrnsteinUhlenbeck
dnPhyloOrnsteinUhlenbeckMVN
dnPhyloOrnsteinUhlenbeckREML
dnPhyloOrnsteinUhlenbeckThreePoint
dnPhyloWhiteNoise
dnPhylodynamicBirthDeathProcess
dnPiecewiseOccurrenceBirthDeath
dnPointMass
dnPoisson
dnReversibleJumpMixture
dnSBBDP
dnScaledDirichlet
dnSoftBoundUniformNormal
dnStudentT
dnTimeVaryingStateDependentSpeciationExtinction
dnUPP
dnUltrametricTree
dnUniform
dnUniformInteger
dnUniformNatural
dnUniformSerialSampledTimeTree
dnUniformTimeTree
dnUniformTopology
dnUniformTopologyBranchLength
dnVarianceGamma
dnWeightedConstrainedNodeOrder
dnWeightedSample
dnWhiteNoise
dnWishart
Functions
UPGMA
VectorMonitors
VectorMoves
[]
abs
ancestralStateTree
annotateTree
append
branchScoreDistance
ceil
characterMapTree
checkNodeOrderConstraints
choose
clear
combineCharacter
computeWeightedNodeOrderConstraintsScore
concatenate
consensusTree
convertCountFileToNaturalNumbers
convertFastaFileToNaturalNumbers
convertToPhylowood
diagonalMatrix
exists
exp
fileExists
floor
fnAdjacentRateModifier
fnAverageDistanceMatrix
fnBetaBrokenStick
fnBinaryMutationCoalescentRateMatrix
fnBiogeoDE
fnBiogeographyCladoEventsBD
fnBiogeographyRateMatrix
fnBlosum62
fnChromosomes
fnChromosomesCladoEventsBD
fnChromosomesCladoProbs
fnChromosomesPloidy
fnChromosomesPloidyCladoEventsBD
fnChronoToPhylo
fnCladeSpecificHierarchicalBranchRate
fnCladogeneticProbabilityMatrix
fnCladogeneticSpeciationRateMatrix
fnCoala
fnCodon
fnCodonGY94
fnCodonHKY
fnCodonMG94
fnCodonMG94K
fnCollapseSA
fnCovarion
fnCovarionRateMatrix
fnCpRev
fnDECCladoProbs
fnDECRateMatrix
fnDECRates
fnDECRoot
fnDayhoff
fnDecompVarCovar
fnDiscretizeBeta
fnDiscretizeBetaQuadrature
fnDiscretizeDistribution
fnDiscretizeGamma
fnDiscretizeGammaFromBetaQuantiles
fnDiscretizeGammaQuadrature
fnDiscretizeLognormalQuadrature
fnDistanceRateModifier
fnDppConcFromMean
fnDppMeanFromConc
fnEarlyBurst
fnEpoch
fnEpochCladoProbs
fnExtantTree
fnF1x4
fnF2x4
fnF3x4
fnF81
fnFMutSel
fnFMutSel0
fnFeatureInformedRates
fnFlowT2Populations
fnFreeBinary
fnFreeK
fnFreeSymmetricRateMatrix
fnGTR
fnGeographicalDistance
fnHKY
fnHiddenStateRateMatrix
fnHostSwitchRateModifier
fnInferAncestralPopSize
fnInfiniteSites
fnJC
fnJones
fnK80
fnK81
fnLG
fnLnProbability
fnMixtureCladoProbs
fnMtMam
fnMtRev
fnMutSel
fnMutSelAA
fnNormalizedQuantile
fnNumUniqueInVector
fnOrderedRateMatrix
fnPD
fnPartialToCorr
fnPattersonsD
fnPhylogeneticIndependentContrasts
fnPhylogeneticIndependentContrastsMultiSample
fnPoMo
fnPoMo2N
fnPoMo4N
fnPoMoKN
fnPruneTree
fnRangeEvolutionRateModifier
fnRateGeneratorSequence
fnReversiblePoMo
fnReversiblePoMo2N
fnReversiblePoMo4N
fnReversiblePoMoBalance4N
fnReversiblePoMoKN
fnReversiblePoMoNeutralM4N
fnReversiblePoMoThree4
fnReversiblePoMoThree4N
fnReversiblePoMoTwo4N
fnRtRev
fnSampledCladogenesisRootFrequencies
fnSegregatingSites
fnShiftEvents
fnShortestDistance
fnSiteRateModifier
fnStateCountRateModifier
fnStirling
fnStitchTree
fnT92
fnTIM
fnTVM
fnTajimasD
fnTajimasPi
fnTrN
fnTreeAssembly
fnTreePairwiseDistances
fnTreePairwiseNodalDistances
fnTreeScale
fnUpperTriangle
fnVT
fnVarCovar
fnWAG
fnWattersonsTheta
fnX2
fnX3
fnassembleContinuousMRF
fndNdS
formatDiscreteCharacterData
gamma
geometricMean
getOption
getwd
help
ifelse
int
license
listFiles
listOptions
ln
loadPlugin
log
logistic
ls
mapTree
matrix
max
maxdiff
maximumTree
mccTree
mean
median
min
module
mrcaIndex
nodeAgeByID
normalize
pomoRF
pomoState4Convert
posteriorPredictiveProbability
power
printSeed
profile
quantile
quit
range
readAncestralStateTrace
readAncestralStateTreeTrace
readAtlas
readBranchLengthTrees
readCharacterData
readContinuousCharacterData
readDelimitedCharacterData
readDelimitedDataFile
readDiscreteCharacterData
readDistanceMatrix
readMatrix
readPoMoCountFile
readRegionalFeatures
readRelativeNodeAgeConstraints
readRelativeNodeAgeWeightedConstraints
readStochasticVariableTrace
readTaxonData
readTrace
readTreeTrace
readTrees
readVCF
rep
reverse
rootedTripletDist
round
seed
seq
setOption
setwd
sigmoid
simCompleteTree
simForwardBirthDeath
simStartingTree
simTree
sinh
sort
source
sqrt
stdev
structure
sum
summarizeCharacterMaps
symmetricDifference
system
tanh
time
tmrca
treeTrace
trunc
type
v
var
vectorFlatten
write
writeDelimitedCharacterData
writeFasta
writeNexus
Moves
mvAVMVN
mvAddRemoveTip
mvBetaProbability
mvBetaSimplex
mvBinarySwitch
mvBirthDeathEvent
mvBirthDeathEventContinuous
mvBirthDeathFromAgeEvent
mvBranchLengthScale
mvBurstEvent
mvCharacterHistory
mvCollapseExpandFossilBranch
mvConjugateInverseWishart
mvContinuousCharacterDataSlide
mvContinuousEventScale
mvCorrelationMatrixElementSwap
mvCorrelationMatrixRandomWalk
mvCorrelationMatrixSingleElementBeta
mvCorrelationMatrixSpecificElementBeta
mvCorrelationMatrixUpdate
mvDPPAllocateAuxGibbs
mvDPPGibbsConcentration
mvDPPValueBetaSimplex
mvDPPValueScaling
mvDPPValueSliding
mvDirichletSimplex
mvDiscreteEventCategoryRandomWalk
mvElementSwapSimplex
mvEllipticalSliceSamplingSimple
mvEmpiricalTree
mvEventTimeBeta
mvEventTimeSlide
mvFNPR
mvGMRFHyperpriorGibbs
mvGMRFUnevenGridHyperpriorGibbs
mvGPR
mvGammaScale
mvGibbsDrawCharacterHistory
mvGibbsMixtureAllocation
mvGraphFlipClique
mvGraphFlipEdge
mvGraphShiftEdge
mvHSRFHyperpriorsGibbs
mvHSRFIntervalSwap
mvHSRFUnevenGridHyperpriorsGibbs
mvHomeologPhase
mvIndependentTopology
mvLayeredScaleProposal
mvLevyJump
mvLevyJumpSum
mvMatrixElementScale
mvMatrixElementSlide
mvMirror
mvMirrorMultiplier
mvMixtureAllocation
mvMultiValueEventBirthDeath
mvMultiValueEventScale
mvMultiValueEventSlide
mvMultipleElementVectorScale
mvNNI
mvNarrow
mvNarrowExchangeRateMatrix
mvNodeRateTimeSlideUniform
mvNodeTimeScale
mvNodeTimeSlideBeta
mvNodeTimeSlidePathTruncatedNormal
mvNodeTimeSlideUniform
mvNodeTimeSlideUniformAgeConstrained
mvOrderedEventBirthDeath
mvOrderedEventScaleRealPos
mvOrderedEventSlideProbability
mvOrderedEventSlideReal
mvOrderedEventSlideRealPos
mvOrderedEventTimeSlide
mvOrderedEventVectorScaleRealPos
mvOrderedEventVectorSlideProbability
mvOrderedEventVectorSlideReal
mvOrderedEventVectorSlideRealPos
mvRJSwitch
mvRandomDive
mvRandomGeometricWalk
mvRandomIntegerWalk
mvRateAgeBetaShift
mvRateAgeProposal
mvRateAgeSubtreeProposal
mvResampleFBD
mvRootTimeScaleBactrian
mvRootTimeSlide
mvRootTimeSlideUniform
mvSPR
mvScale
mvScaleBactrian
mvScaleBactrianCauchy
mvShrinkExpand
mvShrinkExpandScale
mvSlice
mvSlide
mvSlideBactrian
mvSpeciesNarrow
mvSpeciesNodeTimeSlideUniform
mvSpeciesSubtreeScale
mvSpeciesSubtreeScaleBeta
mvSpeciesTreeScale
mvSubtreeScale
mvSubtreeSwap
mvSymmetricMatrixElementSlide
mvSynchronizedVectorFixedSingleElementSlide
mvTipTimeSlideUniform
mvTreeScale
mvUPPAllocation
mvUpDownScale
mvUpDownSlide
mvUpDownSlideBactrian
mvVectorBinarySwitch
mvVectorFixedSingleElementSlide
mvVectorScale
mvVectorSingleElementScale
mvVectorSingleElementSlide
mvVectorSlide
mvVectorSlideRecenter
Monitors
mnAncestralState
mnCharHistoryNewick
mnCharHistoryNhx
mnCharacterHistorySummary
mnExtNewick
mnFile
mnHomeologPhase
mnJointConditionalAncestralState
mnModel
mnNexus
mnProbability
mnScreen
mnSiteMixtureAllocation
mnStochasticBranchRate
mnStochasticBranchStateTimes
mnStochasticCharacterMap
mnStochasticVariable
Workspace Objects
BootstrapAnalysis
CorrespondenceAnalysis
HillClimber
beca
dfConstant
dfExponential
dfLinear
mcmc
mcmcmc
model
pathSampler
posteriorPredictiveAnalysis
posteriorPredictiveSimulation
powerPosterior
srGelmanRubin
srGeweke
srMaxIteration
srMaxTime
srMinESS
srStationarity
steppingStoneSampler
validationAnalysis
RevObject[][]
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