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PCMBase  

Simulation and Likelihood Calculation of Phylogenetic Comparative Models
View on CRAN: Click here


Download and install PCMBase package within the R console
Install from CRAN:
install.packages("PCMBase")

Install from Github:
library("remotes")
install_github("cran/PCMBase")

Install by package version:
library("remotes")
install_version("PCMBase", "1.2.14")



Attach the package and use:
library("PCMBase")
Maintained by
Venelin Mitov
[Scholar Profile | Author Map]
First Published: 2018-12-01
Latest Update: 2022-11-18
Description:
Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for inference of these models to tree and trait data. The package web-site provides access to the documentation and other resources.
How to cite:
Venelin Mitov (2018). PCMBase: Simulation and Likelihood Calculation of Phylogenetic Comparative Models. R package version 1.2.14, https://cran.r-project.org/web/packages/PCMBase. Accessed 13 Apr. 2025.
Previous versions and publish date:
1.2.7 (2018-12-01 00:50), 1.2.9 (2019-03-15 11:43), 1.2.10 (2019-09-11 18:30), 1.2.11 (2019-12-12 20:00), 1.2.12 (2021-06-07 10:00), 1.2.13 (2022-11-18 09:40)
Other packages that cited PCMBase R package
View PCMBase citation profile
Other R packages that PCMBase depends, imports, suggests or enhances
Complete documentation for PCMBase
Functions, R codes and Examples using the PCMBase R package
Some associated functions: Args_MixedGaussian_MGPMDefaultModelTypes . Args_MixedGaussian_MGPMScalarOUType . Args_MixedGaussian_MGPMSurfaceOUType . FormatCellAsLatex . FormatTableAsLatex . MGPMScalarOUType . MGPMSurfaceOUType . MatchListMembers . MixedGaussian . MixedGaussianTemplate . PCM . PCMAbCdEf . PCMAddToListAttribute . PCMApplyTransformation . PCMBaseIsADevRelease . PCMBaseTestObjects . PCMColorPalette . PCMCombineListAttribute . PCMCond.GaussianPCM . PCMCond . PCMCondVOU . PCMCreateLikelihood . PCMDefaultModelTypes . PCMDefaultObject . PCMDescribe . PCMDescribeParameters . PCMExtractDimensions . PCMExtractRegimes . PCMFindMethod . PCMFixParameter . PCMGenerateModelTypes . PCMGenerateParameterizations . PCMGetAttribute . PCMGetVecParamsRegimesAndModels . PCMInfo . PCMLik . PCMLikDmvNorm . PCMLikTrace . PCMListMembers . PCMListParameterizations . PCMLmr . PCMMapModelTypesToRegimes . PCMMean . PCMMeanAtTime . PCMModelTypes . PCMModels . PCMNumRegimes . PCMNumTraits . PCMOptions . PCMPExpxMeanExp . PCMPLambdaP_1 . PCMPairSums . PCMParam . PCMParamCount . PCMParamGetShortVector . PCMParamLoadOrStore . PCMParamLocateInShortVector . PCMParamLowerLimit . PCMParamRandomVecParams . PCMParamSetByName . PCMParamType . PCMParamUpperLimit . PCMParentClasses . PCMParseErrorMessage . PCMPlotGaussianDensityGrid2D . PCMPlotGaussianSample2D . PCMPlotMath . PCMPlotTraitData2D . PCMPresentCoordinates . PCMRegimes . PCMSetAttribute . PCMSim . PCMSpecify . PCMTable . PCMTableParameterizations . PCMTrajectory . PCMTree . PCMTreeBackbonePartition . PCMTreeDropClade . PCMTreeDtNodes . PCMTreeEdgeTimes . PCMTreeEvalNestedEDxOnTree . PCMTreeExtractClade . PCMTreeGetBranchLength . PCMTreeGetDaughters . PCMTreeGetLabels . PCMTreeGetParent . PCMTreeGetPartNames . PCMTreeGetPartRegimes . PCMTreeGetPartition . PCMTreeGetPartsForNodes . PCMTreeGetRegimesForEdges . PCMTreeGetRegimesForNodes . PCMTreeGetTipsInPart . PCMTreeGetTipsInRegime . PCMTreeInsertSingletons . PCMTreeJumps . PCMTreeListAllPartitions . PCMTreeListCladePartitions . PCMTreeListDescendants . PCMTreeListRootPaths . PCMTreeLocateEpochOnBranches . PCMTreeLocateMidpointsOnBranches . PCMTreeMatchLabels . PCMTreeMatrixNodesInSamePart . PCMTreeNearestNodesToEpoch . PCMTreeNodeTimes . PCMTreeNumNodes . PCMTreeNumParts . PCMTreeNumTips . PCMTreePlot . PCMTreePostorder . PCMTreePreorder . PCMTreeSetLabels . PCMTreeSetPartRegimes . PCMTreeSetPartition . PCMTreeSetRegimesForEdges . PCMTreeSplitAtNode . PCMTreeTableAncestors . PCMTreeToString . PCMTreeVCV . PCMUnfixParameter . PCMVar . PCMVarAtTime . TruePositiveRate . UpperTriFactor . White . as.MixedGaussian . dataFig3 . is.GaussianPCM . is.MixedGaussian . is.PCM . is.PCMTree . 
Some associated R codes: AutoGeneratedModelTypes.R . BM.R . BMdrift.R . DOU.R . DefaultModelTypes.R . GaussianPCM.R . JOU.R . LatexTools.R . MixedGaussian.R . OU.R . PCM.R . PCMBaseTestObjects.R . PCMParam.R . PCMTable.R . PCMTree.R . Utilities.R . White.R . matrixparametrizations.R . zzz.R .  Full PCMBase package functions and examples
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