Files in PCMBase
Simulation and Likelihood Calculation of Phylogenetic Comparative Models
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/LatexTools.R
R/PCMTable.R
R/DefaultModelTypes.R
R/matrixparametrizations.R
R/AutoGeneratedModelTypes.R
R/PCM.R
R/Utilities.R
R/PCMTree.R
R/White.R
R/OU.R
R/MixedGaussian.R
R/BM.R
R/zzz.R
R/DOU.R
R/JOU.R
R/BMdrift.R
R/PCMBaseTestObjects.R
R/PCMParam.R
R/GaussianPCM.R
inst/CITATION
inst/doc/PCMCreateModel.R
inst/doc/PCMBase.R
inst/doc/PCMTracePruning.html
inst/doc/PCMTracePruning.Rmd
inst/doc/PCMParam.Rmd
inst/doc/PCMTracePruning.R
inst/doc/PCMBase.Rmd
inst/doc/PCMCreateModel.html
inst/doc/PCMBase.html
inst/doc/PCMCreateModel.Rmd
inst/doc/PCMParam.html
inst/doc/PCMParam.R
build/vignette.rds
tests/testthat.R
tests/README.txt
tests/testthat/test-PCMLik-OU.R
tests/testthat/test-PCMLik-DOU.R
tests/testthat/test-PCMLik-BMdrift.R
tests/testthat/test-PCMLik-BM.R
tests/testthat/test-PCMSim.R
tests/testthat/test-Transformations.R
tests/testthat/test-PCMTree.R
tests/testthat/test-PCM.R
tests/testthat/test-PCMParam.R
tests/testthat/test-MixedGaussian.R
vignettes/PCMBMkappa.zip
vignettes/PCMTracePruning.Rmd
vignettes/PCMParam.Rmd
vignettes/PCMBase.Rmd
vignettes/REFERENCES.bib
vignettes/PCMCreateModel.Rmd
vignettes/REFERENCES-R.bib
vignettes/Fig1.pdf
data/dataFig3.rda
data/PCMBaseTestObjects.rda
man/PCMCond.Rd
man/PCMTreeEdgeTimes.Rd
man/FormatCellAsLatex.Rd
man/PCMTreeEvalNestedEDxOnTree.Rd
man/PCMTreeDropClade.Rd
man/PCMCond.GaussianPCM.Rd
man/TruePositiveRate.Rd
man/PCMParamUpperLimit.Rd
man/PCMParamLocateInShortVector.Rd
man/PCMTreeInsertSingletons.Rd
man/PCMDefaultModelTypes.Rd
man/PCMApplyTransformation.Rd
man/PCMTreeVCV.Rd
man/PCMSim.Rd
man/PCMLikDmvNorm.Rd
man/PCMTreeMatchLabels.Rd
man/FormatTableAsLatex.Rd
man/PCMDescribeParameters.Rd
man/PCMTreeGetBranchLength.Rd
man/PCMParam.Rd
man/PCMColorPalette.Rd
man/PCMVarAtTime.Rd
man/PCMGetAttribute.Rd
man/PCMTreeGetPartNames.Rd
man/PCMTreeGetRegimesForNodes.Rd
man/PCMTreeSetPartRegimes.Rd
man/PCMTreeListDescendants.Rd
man/PCMTreeTableAncestors.Rd
man/PCMLikTrace.Rd
man/PCMTreeNearestNodesToEpoch.Rd
man/as.MixedGaussian.Rd
man/PCMParamGetShortVector.Rd
man/PCMAddToListAttribute.Rd
man/PCMTreeGetLabels.Rd
man/PCMTreeNumParts.Rd
man/PCM.Rd
man/PCMTreeGetPartsForNodes.Rd
man/PCMDefaultObject.Rd
man/PCMPairSums.Rd
man/PCMPlotTraitData2D.Rd
man/PCMTreeLocateMidpointsOnBranches.Rd
man/PCMPExpxMeanExp.Rd
man/PCMTreeGetTipsInRegime.Rd
man/is.PCMTree.Rd
man/PCMTreePreorder.Rd
man/dataFig3.Rd
man/PCMParamRandomVecParams.Rd
man/PCMOptions.Rd
man/PCMTreeGetRegimesForEdges.Rd
man/PCMExtractDimensions.Rd
man/PCMGenerateModelTypes.Rd
man/PCMMean.Rd
man/PCMMeanAtTime.Rd
man/PCMSetAttribute.Rd
man/PCMTreeListAllPartitions.Rd
man/MatchListMembers.Rd
man/PCMPlotGaussianSample2D.Rd
man/PCMModelTypes.Rd
man/PCMVar.Rd
man/PCMExtractRegimes.Rd
man/PCMTreeExtractClade.Rd
man/PCMTreePostorder.Rd
man/PCMPLambdaP_1.Rd
man/PCMTreeGetPartition.Rd
man/PCMFindMethod.Rd
man/PCMParamLowerLimit.Rd
man/PCMPlotGaussianDensityGrid2D.Rd
man/PCMTreeSplitAtNode.Rd
man/MGPMScalarOUType.Rd
man/PCMParseErrorMessage.Rd
man/PCMBaseTestObjects.Rd
man/is.MixedGaussian.Rd
man/PCMTreeGetTipsInPart.Rd
man/PCMTableParameterizations.Rd
man/PCMCreateLikelihood.Rd
man/PCMTrajectory.Rd
man/PCMModels.Rd
man/PCMLik.Rd
man/PCMNumTraits.Rd
man/PCMBaseIsADevRelease.Rd
man/MixedGaussian.Rd
man/PCMParamType.Rd
man/PCMListMembers.Rd
man/PCMFixParameter.Rd
man/PCMTreeNumNodes.Rd
man/PCMPresentCoordinates.Rd
man/PCMTreeListCladePartitions.Rd
man/PCMCombineListAttribute.Rd
man/PCMTreeToString.Rd
man/PCMRegimes.Rd
man/PCMGetVecParamsRegimesAndModels.Rd
man/PCMTreeGetParent.Rd
man/PCMTreeDtNodes.Rd
man/PCMTreeGetDaughters.Rd
man/PCMLmr.Rd
man/PCMTable.Rd
man/PCMAbCdEf.Rd
man/PCMParamCount.Rd
man/PCMUnfixParameter.Rd
man/PCMTreeMatrixNodesInSamePart.Rd
man/PCMNumRegimes.Rd
man/PCMTreeSetRegimesForEdges.Rd
man/PCMGenerateParameterizations.Rd
man/Args_MixedGaussian_MGPMSurfaceOUType.Rd
man/PCMTreeSetPartition.Rd
man/PCMTreeNodeTimes.Rd
man/MGPMSurfaceOUType.Rd
man/PCMTreeLocateEpochOnBranches.Rd
man/PCMSpecify.Rd
man/Args_MixedGaussian_MGPMDefaultModelTypes.Rd
man/PCMCondVOU.Rd
man/MixedGaussianTemplate.Rd
man/PCMInfo.Rd
man/PCMParentClasses.Rd
man/PCMParamLoadOrStore.Rd
man/UpperTriFactor.Rd
man/PCMPlotMath.Rd
man/PCMTreeListRootPaths.Rd
man/PCMListParameterizations.Rd
man/PCMTreeGetPartRegimes.Rd
man/is.GaussianPCM.Rd
man/PCMMapModelTypesToRegimes.Rd
man/PCMParamSetByName.Rd
man/Args_MixedGaussian_MGPMScalarOUType.Rd
man/PCMTreeSetLabels.Rd
man/PCMTreeBackbonePartition.Rd
man/PCMTreeJumps.Rd
man/is.PCM.Rd
man/White.Rd
man/PCMDescribe.Rd
man/PCMTree.Rd
man/PCMTreeNumTips.Rd
man/PCMTreePlot.Rd
