API for PCMBase
Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Global functions
.M.mult.givens Source code
.col.rot Source code
.givens.mult.M Source code
.givens.real Source code
.inv.rho.givens.real Source code
.my_warning Source code
.num.inv.transform.positive Source code
.num.transform.positive Source code
.onLoad Source code
.par.inv.transform.decomp.matrix Source code
.par.inv.transform.decomp.neg.real.matrix Source code
.par.inv.transform.decomp.pos.real.matrix Source code
.par.inv.transform.decomp.real.matrix Source code
.par.inv.transform.decomp.sym.matrix Source code
.par.inv.transform.invert.matrix Source code
.par.inv.transform.invert.qr.matrix Source code
.par.inv.transform.invert.svd.matrix Source code
.par.inv.transform.lowertri.matrix Source code
.par.inv.transform.orth.matrix.cayley Source code
.par.inv.transform.orth.matrix.givens Source code
.par.inv.transform.symmetric.matrix Source code
.par.inv.transform.twobytwo.matrix Source code
.par.inv.transform.uppertri.matrix Source code
.par.transform.decomp.matrix Source code
.par.transform.decomp.neg.real.matrix Source code
.par.transform.decomp.pos.real.matrix Source code
.par.transform.decomp.real.matrix Source code
.par.transform.decomp.sym.matrix Source code
.par.transform.invert.matrix Source code
.par.transform.invert.qr.matrix Source code
.par.transform.invert.svd.matrix Source code
.par.transform.lowertri.matrix Source code
.par.transform.orth.matrix.cayley Source code
.par.transform.orth.matrix.givens Source code
.par.transform.symmetric.matrix Source code
.par.transform.twobytwo.matrix Source code
.par.transform.uppertri.matrix Source code
.row.rot Source code
Args_MixedGaussian_MGPMDefaultModelTypes Man page Source code
Args_MixedGaussian_MGPMScalarOUType Man page Source code
Args_MixedGaussian_MGPMSurfaceOUType Man page Source code
AsRExpression Source code
FalsePositiveRate Man page Source code
FormatCellAsLatex Man page Source code
FormatTableAsLatex Man page Source code
GetSigma_x Source code
MGPMDefaultModelTypes Man page Source code
MGPMScalarOUType Man page Source code
MGPMSurfaceOUType Man page Source code
MatchListMembers Man page Source code
MixedGaussian Man page Source code
MixedGaussianTemplate Man page Source code
PCM Man page Source code
PCM.PCM Source code
PCM.character Source code
PCM.default Source code
PCMAbCdEf Man page
PCMAddToListAttribute Man page Source code
PCMApplyTransformation Man page Source code
PCMApplyTransformation.PCM Source code
PCMApplyTransformation._CholeskyFactor Source code
PCMApplyTransformation._Schur Source code
PCMApplyTransformation.default Source code
PCMBaseIsADevRelease Man page Source code
PCMBaseTestObjects Man page
PCMColorPalette Man page Source code
PCMCombineListAttribute Man page Source code
PCMCond Man page Source code
PCMCond.BM Source code
PCMCond.BM_drift Source code
PCMCond.DOU Source code
PCMCond.GaussianPCM Man page Source code
PCMCond.JOU Source code
PCMCond.MixedGaussian Source code
PCMCond.OU Source code
PCMCond.White Source code
PCMCondVOU Man page
PCMCreateLikelihood Man page Source code
PCMDefaultModelTypes Man page Source code
PCMDefaultObject Man page Source code
PCMDefaultObject.MatrixParameter Source code
PCMDefaultObject.PCM Source code
PCMDefaultObject.ScalarParameter Source code
PCMDefaultObject.VectorParameter Source code
PCMDescribe Man page Source code
PCMDescribe.BM Source code
PCMDescribe.BM_drift Source code
PCMDescribe.DOU Source code
PCMDescribe.JOU Source code
PCMDescribe.MixedGaussian Source code
PCMDescribe.OU Source code
PCMDescribe.PCM Source code
PCMDescribe.White Source code
PCMDescribeParameters Man page Source code
PCMDescribeParameters.BM Source code
PCMDescribeParameters.BM_drift Source code
PCMDescribeParameters.DOU Source code
PCMDescribeParameters.JOU Source code
PCMDescribeParameters.OU Source code
PCMDescribeParameters.White Source code
PCMExtractDimensions Man page Source code
PCMExtractDimensions.MatrixParameter Source code
PCMExtractDimensions.PCM Source code
PCMExtractDimensions.ScalarParameter Source code
PCMExtractDimensions.VectorParameter Source code
PCMExtractRegimes Man page Source code
PCMExtractRegimes.MatrixParameter Source code
PCMExtractRegimes.MixedGaussian Source code
PCMExtractRegimes.PCM Source code
PCMExtractRegimes.ScalarParameter Source code
PCMExtractRegimes.VectorParameter Source code
PCMFindMethod Man page Source code
PCMFixParameter Man page Source code
PCMGenerateModelTypes Man page Source code
PCMGenerateParameterizations Man page Source code
PCMGetAttribute Man page Source code
PCMGetVecParamsRegimesAndModels Man page Source code
PCMGetVecParamsRegimesAndModels.PCM Source code
PCMInfo Man page Source code
PCMInfo.PCM Source code
PCMInfo.White Source code
PCMLik Man page Source code
PCMLik.GaussianPCM Source code
PCMLikDmvNorm Man page Source code
PCMLikTrace Man page Source code
PCMLikTrace.GaussianPCM Source code
PCMListDefaultParameterizations Man page Source code
PCMListDefaultParameterizations.BM Source code
PCMListDefaultParameterizations.BM_drift Source code
PCMListDefaultParameterizations.OU Source code
PCMListDefaultParameterizations.default Source code
PCMListMembers Man page Source code
PCMListParameterizations Man page Source code
PCMListParameterizations.BM Source code
PCMListParameterizations.BM_drift Source code
PCMListParameterizations.DOU Source code
PCMListParameterizations.JOU Source code
PCMListParameterizations.OU Source code
PCMListParameterizations.White Source code
PCMLmr Man page
PCMMapModelTypesToRegimes Man page Source code
PCMMapModelTypesToRegimes.MixedGaussian Source code
PCMMapModelTypesToRegimes.PCM Source code
PCMMean Man page Source code
PCMMean.GaussianPCM Source code
PCMMeanAtTime Man page Source code
PCMModelTypes Man page Source code
PCMModelTypes.MixedGaussian Source code
PCMModelTypes.PCM Source code
PCMModels Man page Source code
PCMNumRegimes Man page Source code
PCMNumRegimes.MatrixParameter Source code
PCMNumRegimes.PCM Source code
PCMNumRegimes.PCMTree Source code
PCMNumRegimes.ScalarParameter Source code
PCMNumRegimes.VectorParameter Source code
PCMNumRegimes.phylo Source code
PCMNumTraits Man page Source code
PCMNumTraits.MatrixParameter Source code
PCMNumTraits.PCM Source code
PCMNumTraits.ScalarParameter Source code
PCMNumTraits.VectorParameter Source code
PCMOptions Man page Source code
PCMPExpxMeanExp Man page
PCMPLambdaP_1 Man page
PCMPairSums Man page
PCMParam Man page
PCMParamCount Man page Source code
PCMParamCount.MatrixParameter Source code
PCMParamCount.MixedGaussian Source code
PCMParamCount.PCM Source code
PCMParamCount.ScalarParameter Source code
PCMParamCount.VectorParameter Source code
PCMParamGetShortVector Man page Source code
PCMParamGetShortVector.PCM Source code
PCMParamGetShortVector.default Source code
PCMParamLoadOrStore Man page Source code
PCMParamLoadOrStore.MatrixParameter Source code
PCMParamLoadOrStore.PCM Source code
PCMParamLoadOrStore.ScalarParameter Source code
PCMParamLoadOrStore.VectorParameter Source code
PCMParamLocateInShortVector Man page Source code
PCMParamLowerLimit Man page Source code
PCMParamLowerLimit.PCM Source code
PCMParamLowerLimit._NonNegative Source code
PCMParamLowerLimit._WithNonNegativeDiagonal Source code
PCMParamLowerLimit.default Source code
PCMParamRandomVecParams Man page Source code
PCMParamRandomVecParams.default Source code
PCMParamSetByName Man page Source code
PCMParamSetByName.PCM Source code
PCMParamType Man page
PCMParamUpperLimit Man page Source code
PCMParamUpperLimit.PCM Source code
PCMParamUpperLimit.default Source code
PCMParentClasses Man page Source code
PCMParentClasses.BM Source code
PCMParentClasses.BM__Global_X0__Diagonal_WithNonNegativeDiagonal Source code Source code Source code
PCMParentClasses.BM__Global_X0__ScalarDiagonal_WithNonNegativeDi Source code Source code Source code
PCMParentClasses.BM__Global_X0__UpperTriangularWithDiagonal_With Source code Source code Source code
PCMParentClasses.BM__Omitted_X0__Diagonal_WithNonNegativeDiagona Source code Source code Source code
PCMParentClasses.BM__Omitted_X0__ScalarDiagonal_WithNonNegativeD Source code Source code Source code
PCMParentClasses.BM__Omitted_X0__UpperTriangularWithDiagonal_Wit Source code Source code Source code
PCMParentClasses.BM_drift Source code
PCMParentClasses.DOU Source code
PCMParentClasses.GaussianPCM Source code
PCMParentClasses.JOU Source code
PCMParentClasses.MixedGaussian Source code
PCMParentClasses.OU Source code
PCMParentClasses.OU__Global_X0__Diagonal_WithNonNegativeDiagonal Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__Global_H__Theta__Diagonal_WithNo Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__Global_H__Theta__ScalarDiagonal_ Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__Global_H__Theta__UpperTriangular Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__H__Theta__Diagonal_WithNonNegati Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__H__Theta__ScalarDiagonal_WithNon Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__H__Theta__UpperTriangularWithDia Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__Schur_Diagonal_WithNonNegativeDi Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__Schur_ScalarDiagonal_WithNonNega Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__Schur_UpperTriangularWithDiagona Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Global_X0__Schur_WithNonNegativeDiagonal_Tr Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Diagonal_WithNonNegativeDiagona Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Global_H__Theta__Diagonal_WithN Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Global_H__Theta__ScalarDiagonal Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Global_H__Theta__UpperTriangula Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__H__Theta__Diagonal_WithNonNegat Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__H__Theta__ScalarDiagonal_WithNo Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__H__Theta__UpperTriangularWithDi Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Schur_Diagonal_WithNonNegativeD Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Schur_ScalarDiagonal_WithNonNeg Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Schur_UpperTriangularWithDiagon Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.OU__Omitted_X0__Schur_WithNonNegativeDiagonal_T Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMParentClasses.PCM Source code
PCMParentClasses.White Source code
PCMParentClasses.White__AllEqual_Global_X0__Diagonal_WithNonNega Source code Source code
PCMParentClasses.White__AllEqual_Global_X0__ScalarDiagonal_WithN Source code Source code
PCMParentClasses.White__AllEqual_Global_X0__UpperTriangularWithD Source code Source code
PCMParentClasses.White__Fixed_Global_X0__Diagonal_WithNonNegativ Source code Source code
PCMParentClasses.White__Fixed_Global_X0__ScalarDiagonal_WithNonN Source code Source code
PCMParentClasses.White__Fixed_Global_X0__UpperTriangularWithDiag Source code Source code
PCMParentClasses.White__Global_X0__Diagonal_WithNonNegativeDiago Source code Source code
PCMParentClasses.White__Global_X0__ScalarDiagonal_WithNonNegativ Source code Source code
PCMParentClasses.White__Global_X0__UpperTriangularWithDiagonal_W Source code Source code
PCMParentClasses.White__Omitted_X0__Diagonal_WithNonNegativeDiag Source code Source code
PCMParentClasses.White__Omitted_X0__ScalarDiagonal_WithNonNegati Source code Source code
PCMParentClasses.White__Omitted_X0__UpperTriangularWithDiagonal_ Source code Source code
PCMParseErrorMessage Man page Source code
PCMPlotGaussianDensityGrid2D Man page Source code
PCMPlotGaussianSample2D Man page Source code
PCMPlotMath Man page Source code
PCMPlotMath.MatrixParameter Source code
PCMPlotMath.PCM Source code
PCMPlotMath.VectorParameter Source code
PCMPlotMath.default Source code
PCMPlotTraitData2D Man page Source code
PCMPresentCoordinates Man page Source code
PCMRegimes Man page Source code
PCMRegimes.PCM Source code
PCMRegimes.PCMTree Source code
PCMRegimes.phylo Source code
PCMSetAttribute Man page Source code
PCMSim Man page Source code
PCMSim.GaussianPCM Source code
PCMSpecify Man page Source code
PCMSpecify.BM Source code
PCMSpecify.BM__Global_X0__Diagonal_WithNonNegativeDiagonal_Sigma Source code Source code Source code
PCMSpecify.BM__Global_X0__ScalarDiagonal_WithNonNegativeDiagonal Source code Source code Source code
PCMSpecify.BM__Global_X0__UpperTriangularWithDiagonal_WithNonNeg Source code Source code Source code
PCMSpecify.BM__Omitted_X0__Diagonal_WithNonNegativeDiagonal_Sigm Source code Source code Source code
PCMSpecify.BM__Omitted_X0__ScalarDiagonal_WithNonNegativeDiagona Source code Source code Source code
PCMSpecify.BM__Omitted_X0__UpperTriangularWithDiagonal_WithNonNe Source code Source code Source code
PCMSpecify.BM_drift Source code
PCMSpecify.DOU Source code
PCMSpecify.JOU Source code
PCMSpecify.OU Source code
PCMSpecify.OU__Global_X0__Diagonal_WithNonNegativeDiagonal_Globa Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Diagonal_WithNonNegativeDiagonal_H__Th Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Global_H__Theta__Diagonal_WithNonNegat Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Global_H__Theta__ScalarDiagonal_WithNo Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Global_H__Theta__UpperTriangularWithDi Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__H__Theta__Diagonal_WithNonNegativeDiag Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__H__Theta__ScalarDiagonal_WithNonNegati Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__H__Theta__UpperTriangularWithDiagonal_ Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Schur_Diagonal_WithNonNegativeDiagonal Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Schur_ScalarDiagonal_WithNonNegativeDi Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Schur_UpperTriangularWithDiagonal_With Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Global_X0__Schur_WithNonNegativeDiagonal_Transfor Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Diagonal_WithNonNegativeDiagonal_Glob Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Diagonal_WithNonNegativeDiagonal_H__T Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Global_H__Theta__Diagonal_WithNonNega Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Global_H__Theta__ScalarDiagonal_WithN Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Global_H__Theta__UpperTriangularWithD Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__H__Theta__Diagonal_WithNonNegativeDia Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__H__Theta__ScalarDiagonal_WithNonNegat Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__H__Theta__UpperTriangularWithDiagonal Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Schur_Diagonal_WithNonNegativeDiagona Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Schur_ScalarDiagonal_WithNonNegativeD Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Schur_UpperTriangularWithDiagonal_Wit Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.OU__Omitted_X0__Schur_WithNonNegativeDiagonal_Transfo Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PCMSpecify.White Source code
PCMSpecify.White__AllEqual_Global_X0__Diagonal_WithNonNegativeDi Source code Source code
PCMSpecify.White__AllEqual_Global_X0__ScalarDiagonal_WithNonNega Source code Source code
PCMSpecify.White__AllEqual_Global_X0__UpperTriangularWithDiagona Source code Source code
PCMSpecify.White__Fixed_Global_X0__Diagonal_WithNonNegativeDiago Source code Source code
PCMSpecify.White__Fixed_Global_X0__ScalarDiagonal_WithNonNegativ Source code Source code
PCMSpecify.White__Fixed_Global_X0__UpperTriangularWithDiagonal_W Source code Source code
PCMSpecify.White__Global_X0__Diagonal_WithNonNegativeDiagonal_Gl Source code
PCMSpecify.White__Global_X0__Diagonal_WithNonNegativeDiagonal_Si Source code
PCMSpecify.White__Global_X0__ScalarDiagonal_WithNonNegativeDiago Source code Source code
PCMSpecify.White__Global_X0__UpperTriangularWithDiagonal_WithNon Source code Source code
PCMSpecify.White__Omitted_X0__Diagonal_WithNonNegativeDiagonal_G Source code
PCMSpecify.White__Omitted_X0__Diagonal_WithNonNegativeDiagonal_S Source code
PCMSpecify.White__Omitted_X0__ScalarDiagonal_WithNonNegativeDiag Source code Source code
PCMSpecify.White__Omitted_X0__UpperTriangularWithDiagonal_WithNo Source code Source code
PCMTable Man page Source code
PCMTable.MixedGaussian Source code
PCMTable.PCM Source code
PCMTableParameterizations Man page Source code
PCMTrajectory Man page Source code
PCMTree Man page Source code
PCMTreeBackbonePartition Man page Source code
PCMTreeDropClade Man page Source code
PCMTreeDtNodes Man page Source code
PCMTreeEdgeTimes Man page Source code
PCMTreeEvalNestedEDxOnTree Man page Source code
PCMTreeExtractClade Man page Source code
PCMTreeGetBranchLength Man page Source code
PCMTreeGetDaughters Man page Source code
PCMTreeGetLabels Man page Source code
PCMTreeGetNodeLabels Man page Source code
PCMTreeGetParent Man page Source code
PCMTreeGetPartNames Man page Source code
PCMTreeGetPartRegimes Man page Source code
PCMTreeGetPartition Man page Source code
PCMTreeGetPartsForNodes Man page Source code
PCMTreeGetRegimesForEdges Man page Source code
PCMTreeGetRegimesForNodes Man page Source code
PCMTreeGetRootLabel Man page Source code
PCMTreeGetTipLabels Man page Source code
PCMTreeGetTipsInPart Man page Source code
PCMTreeGetTipsInRegime Man page Source code
PCMTreeInsertSingletons Man page Source code
PCMTreeInsertSingletonsAtEpoch Man page Source code
PCMTreeInsertTipsOrSingletons Man page Source code
PCMTreeJumps Man page Source code
PCMTreeListAllPartitions Man page Source code
PCMTreeListAllPartitionsInternal Source code
PCMTreeListCladePartitions Man page Source code
PCMTreeListDescendants Man page Source code
PCMTreeListRootPaths Man page Source code
PCMTreeLocateEpochOnBranches Man page Source code
PCMTreeLocateMidpointsOnBranches Man page Source code
PCMTreeMatchLabels Man page Source code
PCMTreeMatrixNodesInSamePart Man page Source code
PCMTreeMatrixNodesInSameRegime Man page Source code
PCMTreeNearestNodesToEpoch Man page Source code
PCMTreeNodeTimes Man page Source code
PCMTreeNumNodes Man page Source code
PCMTreeNumParts Man page Source code
PCMTreeNumTips Man page Source code
PCMTreePlot Man page Source code
PCMTreePostorder Man page Source code
PCMTreePreorder Man page Source code
PCMTreeSetLabels Man page Source code
PCMTreeSetPartRegimes Man page Source code
PCMTreeSetPartition Man page Source code
PCMTreeSetRegimesForEdges Man page Source code
PCMTreeSplitAtNode Man page Source code
PCMTreeTableAncestors Man page Source code
PCMTreeToString Man page Source code
PCMTreeVCV Man page Source code
PCMUnfixParameter Man page Source code
PCMVar Man page Source code
PCMVar.GaussianPCM Source code
PCMVarAtTime Man page Source code
TableForRegime Source code
TruePositiveRate Man page Source code
UpperTriFactor Man page Source code
White Man page
`%store%` Source code
`+.PCMTree` Source code
as.MixedGaussian Man page Source code
as.phylo.PCMTree Source code
dataFig3 Man page
format.PCM Source code
is.AllEqual Man page Source code
is.CholeskyFactor Man page Source code
is.Diagonal Man page Source code
is.Fixed Man page Source code
is.GaussianPCM Man page Source code
is.Global Man page Source code
is.Identity Man page Source code
is.Local Man page Source code
is.LowerTriangular Man page Source code
is.LowerTriangularWithDiagonal Man page Source code
is.MatrixParameter Man page Source code
is.MixedGaussian Man page Source code
is.NonNegative Man page Source code
is.Omitted Man page Source code
is.Ones Man page Source code
is.PCM Man page Source code
is.PCMTree Man page Source code
is.ScalarDiagonal Man page Source code
is.ScalarParameter Man page Source code
is.Schur Man page Source code
is.SemiPositiveDefinite Man page Source code
is.Symmetric Man page Source code
is.Transformable Man page Source code
is.Transformed Man page Source code
is.UpperTriangular Man page Source code
is.UpperTriangularWithDiagonal Man page Source code
is.VectorParameter Man page Source code
is.WithCustomVecParams Man page Source code
is.WithNonNegativeDiagonal Man page Source code
is.Zeros Man page Source code
logLik.PCM Source code
print.PCM Source code
print.PCMTable Source code
PCMBase documentation built on Nov. 18, 2022, 9:06 a.m.