Man pages for venelin/PCMBase
Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Args_MixedGaussian_MGPMDefaultModelTypesArguments to be passed to the constructor MixedGaussian when...
Args_MixedGaussian_MGPMScalarOUTypeArguments for the MixedGaussian constructor for scalar OU...
Args_MixedGaussian_MGPMSurfaceOUTypeArguments for the MixedGaussian constructor for SURFACE OU...
dataFig3Data for Fig3 in the TPB manuscript
FormatCellAsLatexLatex representation of a model parameter or other found in a...
FormatTableAsLatexLatex representation of a data.table with matrix and vectors...
is.MixedGaussianCheck if an object is a 'MixedGaussian' PCM
is.PCMCheck if an object is a PCM.
is.PCMTreeCheck that a tree is a PCMTree
MatchListMembersFind the members in a list matching a member expression
MGPMScalarOUTypeClass name for the scalar OU MGPM model type
MGPMSurfaceOUTypeClass name for the SURFACE OU MGPM model type
MixedGaussianCreate a multi-regime Gaussian model (MixedGaussian)
PCMCreate a phylogenetic comparative model object
PCMAbCdEfQuadratic polynomial parameters A, b, C, d, E, f for each...
PCMAddToListAttributeAdd a value to a list-valued attribute of a member or members...
PCMApplyTransformationMap a parametrization to its original form.
PCMBaseIsADevReleaseCheck if the PCMBase version corresponds to a dev release
PCMBaseTestObjectsTest objects for the PCMBase package
PCMColorPaletteA fixed palette of n colors
PCMCombineListAttributeCombine all member attributes of a given name into a list
PCMCondConditional distribution of a daughter node given its parent...
PCMCond.GaussianPCMConditional distribution of a daughter node given its parent...
PCMCondVOUVariance-covariance matrix of an OU process with optional...
PCMCreateLikelihoodCreate a likelihood function of a numerical vector parameter
PCMDefaultModelTypesClass names for the the default PCM and MGPM model types
PCMDefaultObjectGenerate a default object of a given PCM model type or...
PCMDescribeHuman friendly description of a PCM
PCMDescribeParametersDescribe the parameters of a PCM
PCMExtractDimensionsGiven a PCM or a parameter object, extract an analogical...
PCMExtractRegimesGiven a PCM or a parameter object, extract an analogical...
PCMFindMethodFind the S3 method for a given PCM object or class-name and...
PCMFixParameterFix a parameter in a PCM model
PCMGenerateModelTypesGenerate default model types for given PCM base-classes
PCMGenerateParameterizationsGenerate possible parameterizations for a given type of model
PCMGetAttributeValue of an attribute of an object or values for an attribute...
PCMGetVecParamsRegimesAndModelsGet a vector of all parameters (real and discrete) describing...
PCMInfoMeta-information about a tree and trait data associated with...
PCMLikLikelihood of a multivariate Gaussian phylogenetic...
PCMLikDmvNormCalculate the likelihood of a model using the standard...
PCMLikTraceTracing the log-likelihood calculation of a model over each...
PCMListMembersA vector of access-code strings to all members of a named...
PCMListParameterizationsSpecify the parameterizations for each parameter of a model
PCMLmrQuadratic polynomial parameters L, m, r
PCMMapModelTypesToRegimesInteger vector giving the model type index for each regime
PCMMeanExpected mean vector at each tip conditioned on a trait-value...
PCMMeanAtTimeCalculate the mean at time t, given X0, under a PCM model
PCMModelsGet a list of PCM models currently implemented
PCMModelTypesGet the model type(s) of a model
PCMNumRegimesNumber of regimes in a obj
PCMNumTraitsNumber of traits modeled by a PCM
PCMOptionsGlobal options for the PCMBase package
PCMPairSumsSums of pairs of elements in a vector
PCMParamModule PCMParam
PCMParamCountCount the number of free parameters associated with a PCM or...
PCMParamGetShortVectorGet a vector of the variable numeric parameters in a model
PCMParamLoadOrStoreLoad (or store) a PCM parameter from (or to) a vector of the...
PCMParamLocateInShortVectorLocate a named parameter in the short vector representation...
PCMParamLowerLimitThe lower limit for a given model or parameter type
PCMParamRandomVecParamsGenerate a random parameter vector for a model using uniform...
PCMParamSetByNameSet model parameters from a named list
PCMParamTypeParameter types
PCMParamUpperLimitThe upper limit for a given model or parameter type
PCMParentClassesParent S3 classes for a model class
PCMParseErrorMessageExtract error information from a formatted error message.
PCMPExpxMeanExpCreate a function of time that calculates...
PCMPLambdaP_1Eigen-decomposition of a matrix H
PCMPlotGaussianDensityGrid2DA 2D Gaussian distribution density grid in the form of a...
PCMPlotGaussianSample2DA 2D sample from Gaussian distribution
PCMPlotMathBeautiful model description based on plotmath
PCMPlotTraitData2DScatter plot of 2-dimensional data
PCMPresentCoordinatesDetermine which traits are present (active) on each node of...
PCMRegimesGet the regimes (aka colors) of a PCM or of a PCMTree object
PCMSetAttributeSet an attribute of a named member in a PCM or other named...
PCMSimSimulation of a phylogenetic comparative model on a tree
PCMSpecifyParameter specification of PCM model
PCMTableA data.table representation of a PCM object
PCMTableParameterizationsCartesian product of possible parameterizations for the...
PCMTrajectoryGenerate a trajectory for the mean in one regime of a PCM
PCMTreeCreate a PCMTree object from a phylo object
PCMTreeBackbonePartitionPrune the tree leaving one tip for each or some of its parts
PCMTreeDropCladeDrop a clade from a phylogenetic tree
PCMTreeDtNodesA data.table with time, part and regime information for the...
PCMTreeEdgeTimesA matrix with the begin and end time from the root for each...
PCMTreeEvalNestedEDxOnTreePerfrorm nested extractions or drops of clades from a tree
PCMTreeExtractCladeExtract a clade from phylogenetic tree
PCMTreeGetBranchLengthThe length of the branch leading to a node
PCMTreeGetDaughtersA vector of the daughter nodes for a given parent node id in...
PCMTreeGetLabelsGet a vector of the tip and node labels in a tree
PCMTreeGetParentThe parent node id of a daughter node in a tree
PCMTreeGetPartitionGet the starting branch' nodes for each part on a tree
PCMTreeGetPartNamesUnique parts on a tree in the order of occurrence from the...
PCMTreeGetPartRegimesRegime mapping for the parts in a tree
PCMTreeGetPartsForNodesGet the parts of the branches leading to a set of nodes or...
PCMTreeGetRegimesForEdgesModel regimes (i.e. colors) associated with the branches in a...
PCMTreeGetRegimesForNodesGet the regimes of the branches leading to a set of nodes or...
PCMTreeGetTipsInPartGet the tips belonging to a part in a tree
PCMTreeGetTipsInRegimeGet the tips belonging to a regime in a tree
PCMTreeInsertSingletonsInsert singleton nodes on chosen edges
PCMTreeJumpsJumps in modeled traits associated with branches in a tree
PCMTreeListAllPartitionsA list of all possible (including recursive) partitions of a...
PCMTreeListCladePartitionsA list of all possible clade partitions of a tree with a...
PCMTreeListDescendantsA list of the descendants for each node in a tree
PCMTreeListRootPathsA list of the path to the root from each node in a tree
PCMTreeLocateEpochOnBranchesFind the crossing points of an epoch-time with each lineage...
PCMTreeLocateMidpointsOnBranchesFind the middle point of each branch longer than a threshold
PCMTreeMatchLabelsGet the node numbers associated with tip- or node-labels in a...
PCMTreeMatrixNodesInSamePartWhich couples from a given set of nodes in a tree belong to...
PCMTreeNearestNodesToEpochFind the nearest node to a given time from the root (epoch)...
PCMTreeNodeTimesCalculate the time from the root to each node of the tree
PCMTreeNumNodesNumber of all nodes in a tree
PCMTreeNumPartsNumber of unique parts on a tree
PCMTreeNumTipsWrapper for length(tree$tip.label)
PCMTreePlotPlot a tree with parts and regimes assigned to these parts
PCMTreePostorderPost-order tree traversal
PCMTreePreorderPre-order tree traversal
PCMTreeSetLabelsSet tip and internal node labels in a tree
PCMTreeSetPartitionSet a partition of a tree by specifying the partition nodes
PCMTreeSetPartRegimesSet regimes for the parts in a tree
PCMTreeSetRegimesForEdgesSet the regime for each individual edge in a tree explicitly
PCMTreeSplitAtNodeSlit a tree at a given internal node into a clade rooted at...
PCMTreeTableAncestorsA matrix (table) of ancestors/descendants for each node in a...
PCMTreeToStringA character representation of a phylo object.
PCMTreeVCVPhylogenetic Variance-covariance matrix
PCMUnfixParameterUnfix a parameter in a PCM model
PCMVarExpected variance-covariance matrix for each couple of tips...
PCMVarAtTimeCalculate the variance covariance k x k matrix at time t,...
TruePositiveRateTrue positive rate of a set of binary predictions against...
UpperTriFactorUpper triangular factor of a symmetric positive definite...
WhiteWhite Gaussian PCM ignoring phylogenetic history
venelin/PCMBase documentation built on Nov. 13, 2019, 11:20 p.m.