# Generated by roxygen2: do not edit by hand

S3method(PCM,PCM)
S3method(PCM,character)
S3method(PCM,default)
S3method(PCMAbCdEf,default)
S3method(PCMApplyTransformation,"_CholeskiFactor")
S3method(PCMApplyTransformation,"_Schur")
S3method(PCMApplyTransformation,PCM)
S3method(PCMApplyTransformation,default)
S3method(PCMCond,BM)
S3method(PCMCond,DOU)
S3method(PCMCond,GaussianPCM)
S3method(PCMCond,JOU)
S3method(PCMCond,MixedGaussian)
S3method(PCMCond,OU)
S3method(PCMCond,White)
S3method(PCMDefaultObject,MatrixParameter)
S3method(PCMDefaultObject,PCM)
S3method(PCMDefaultObject,ScalarParameter)
S3method(PCMDefaultObject,VectorParameter)
S3method(PCMDescribe,BM)
S3method(PCMDescribe,DOU)
S3method(PCMDescribe,JOU)
S3method(PCMDescribe,MixedGaussian)
S3method(PCMDescribe,OU)
S3method(PCMDescribe,PCM)
S3method(PCMDescribe,White)
S3method(PCMDescribeParameters,BM)
S3method(PCMDescribeParameters,DOU)
S3method(PCMDescribeParameters,JOU)
S3method(PCMDescribeParameters,OU)
S3method(PCMDescribeParameters,White)
S3method(PCMGetVecParamsRegimesAndModels,PCM)
S3method(PCMInfo,PCM)
S3method(PCMInfo,White)
S3method(PCMLik,GaussianPCM)
S3method(PCMListParameterizations,BM)
S3method(PCMListParameterizations,DOU)
S3method(PCMListParameterizations,JOU)
S3method(PCMListParameterizations,OU)
S3method(PCMListParameterizations,White)
S3method(PCMLmr,default)
S3method(PCMMapModelTypesToRegimes,MixedGaussian)
S3method(PCMMapModelTypesToRegimes,PCM)
S3method(PCMMean,GaussianPCM)
S3method(PCMNumRegimes,PCM)
S3method(PCMNumTraits,PCM)
S3method(PCMParamCount,MatrixParameter)
S3method(PCMParamCount,MixedGaussian)
S3method(PCMParamCount,PCM)
S3method(PCMParamCount,ScalarParameter)
S3method(PCMParamCount,VectorParameter)
S3method(PCMParamGetShortVector,PCM)
S3method(PCMParamGetShortVector,default)
S3method(PCMParamLoadOrStore,MatrixParameter)
S3method(PCMParamLoadOrStore,PCM)
S3method(PCMParamLoadOrStore,ScalarParameter)
S3method(PCMParamLoadOrStore,VectorParameter)
S3method(PCMParamLowerLimit,"_WithNonNegativeDiagonal")
S3method(PCMParamLowerLimit,PCM)
S3method(PCMParamLowerLimit,default)
S3method(PCMParamRandomVecParams,default)
S3method(PCMParamSetByName,PCM)
S3method(PCMParamUpperLimit,PCM)
S3method(PCMParamUpperLimit,default)
S3method(PCMParentClasses,BM)
S3method(PCMParentClasses,DOU)
S3method(PCMParentClasses,GaussianPCM)
S3method(PCMParentClasses,JOU)
S3method(PCMParentClasses,MixedGaussian)
S3method(PCMParentClasses,OU)
S3method(PCMParentClasses,PCM)
S3method(PCMParentClasses,White)
S3method(PCMPlotMath,MatrixParameter)
S3method(PCMPlotMath,PCM)
S3method(PCMPlotMath,VectorParameter)
S3method(PCMPlotMath,default)
S3method(PCMRegimes,PCM)
S3method(PCMSim,GaussianPCM)
S3method(PCMSpecify,BM)
S3method(PCMSpecify,DOU)
S3method(PCMSpecify,JOU)
S3method(PCMSpecify,OU)
S3method(PCMSpecify,White)
S3method(PCMVar,GaussianPCM)
S3method(logLik,PCM)
S3method(print,PCM)
export(MixedGaussian)
export(PCM)
export(PCMAbCdEf)
export(PCMApplyTransformation)
export(PCMBaseIsADevRelease)
export(PCMColorPalette)
export(PCMCond)
export(PCMCondVOU)
export(PCMCreateLikelihood)
export(PCMDefaultObject)
export(PCMDescribe)
export(PCMDescribeParameters)
export(PCMFixParameter)
export(PCMGenerateParameterizations)
export(PCMGetVecParamsRegimesAndModels)
export(PCMInfo)
export(PCMLik)
export(PCMListParameterizations)
export(PCMLmr)
export(PCMMapModelTypesToRegimes)
export(PCMMean)
export(PCMMeanAtTime)
export(PCMModels)
export(PCMNumRegimes)
export(PCMNumTraits)
export(PCMOptions)
export(PCMParamCount)
export(PCMParamGetShortVector)
export(PCMParamLoadOrStore)
export(PCMParamLowerLimit)
export(PCMParamRandomVecParams)
export(PCMParamSetByName)
export(PCMParamUpperLimit)
export(PCMParentClasses)
export(PCMParseErrorMessage)
export(PCMPlotGaussianDensityGrid2D)
export(PCMPlotGaussianSample2D)
export(PCMPlotMath)
export(PCMPlotTraitData2D)
export(PCMPresentCoordinates)
export(PCMRegimes)
export(PCMSim)
export(PCMSpecify)
export(PCMTableParameterizations)
export(PCMTreeDropClade)
export(PCMTreeDtNodeRegimes)
export(PCMTreeEdgeTimes)
export(PCMTreeEvalNestedEDxOnTree)
export(PCMTreeExtractBackboneRegimes)
export(PCMTreeExtractClade)
export(PCMTreeGetBranchLength)
export(PCMTreeGetDaughters)
export(PCMTreeGetLabels)
export(PCMTreeGetParent)
export(PCMTreeGetRegimeForNode)
export(PCMTreeGetStartingNodesRegimes)
export(PCMTreeGetTipsInRegime)
export(PCMTreeInsertSingletons)
export(PCMTreeInsertSingletonsAtEpoch)
export(PCMTreeJumps)
export(PCMTreeListCladePartitions)
export(PCMTreeListDescendants)
export(PCMTreeListRootPaths)
export(PCMTreeLocateEpochOnBranches)
export(PCMTreeLocateMidpointsOnBranches)
export(PCMTreeMatchLabels)
export(PCMTreeMatrixNodesInSameRegime)
export(PCMTreeMatrixTipsInSameRegime)
export(PCMTreeNearestNodesToEpoch)
export(PCMTreeNodeTimes)
export(PCMTreeNumNodes)
export(PCMTreeNumTips)
export(PCMTreeNumUniqueRegimes)
export(PCMTreePlot)
export(PCMTreePostorder)
export(PCMTreePreorder)
export(PCMTreeSetDefaultRegime)
export(PCMTreeSetLabels)
export(PCMTreeSetRegimes)
export(PCMTreeSplitAtNode)
export(PCMTreeTableAncestors)
export(PCMTreeToString)
export(PCMTreeUniqueRegimes)
export(PCMUnfixParameter)
export(PCMVar)
export(PCMVarAtTime)
export(is.AllEqual)
export(is.CholeskiFactor)
export(is.Diagonal)
export(is.Fixed)
export(is.Global)
export(is.Identity)
export(is.Local)
export(is.LowerTriangular)
export(is.LowerTriangularWithDiagonal)
export(is.MatrixParameter)
export(is.MixedGaussian)
export(is.NonNegative)
export(is.Omitted)
export(is.Ones)
export(is.PCM)
export(is.ScalarDiagonal)
export(is.ScalarParameter)
export(is.Schur)
export(is.SemiPositiveDefinite)
export(is.Symmetric)
export(is.Transformable)
export(is.Transformed)
export(is.UpperTriangular)
export(is.UpperTriangularWithDiagonal)
export(is.VectorParameter)
export(is.WithCustomVecParams)
export(is.WithNonNegativeDiagonal)
export(is.Zeros)
importFrom(ape,bind.tree)
importFrom(ape,drop.tip)
importFrom(ape,is.ultrametric)
importFrom(ape,mrca)
importFrom(ape,rtree)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,is.data.table)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(expm,expm)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,geom_contour)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_gray)
importFrom(grDevices,hcl)
importFrom(mvtnorm,dmvnorm)
importFrom(mvtnorm,rmvnorm)
importFrom(stats,runif)
importFrom(utils,capture.output)
importFrom(utils,methods)
importFrom(utils,packageDescription)
importFrom(utils,str)
