Function reference • PCMBase

All functions
`Args_MixedGaussian_MGPMDefaultModelTypes()`	Arguments to be passed to the constructor MixedGaussian when constructing a MGPM model with some of the default MGPM model types.
`Args_MixedGaussian_MGPMScalarOUType()`	Arguments for the MixedGaussian constructor for scalar OU MGPM models.
`Args_MixedGaussian_MGPMSurfaceOUType()`	Arguments for the MixedGaussian constructor for SURFACE OU MGPM models.
`as.MixedGaussian()`	Convert a `GaussianPCM` model object to a `MixedGaussian` model object
`dataFig3`	Data for Fig3 in the TPB manuscript
`FormatCellAsLatex()`	Latex representation of a model parameter or other found in a data.table object
`FormatTableAsLatex()`	Latex representation of a data.table with matrix and vectors in its cells
`is.GaussianPCM()`	Check if an object is a `GaussianPCM`
`is.MixedGaussian()`	Check if an object is a `MixedGaussian` PCM
`is.PCM()`	Check if an object is a PCM.
`is.PCMTree()`	Check that a tree is a PCMTree
`MatchListMembers()`	Find the members in a list matching a member expression
`MGPMScalarOUType()`	Class name for the scalar OU MGPM model type
`MGPMSurfaceOUType()`	Class name for the SURFACE OU MGPM model type
`MixedGaussian()`	Create a multi-regime Gaussian model (MixedGaussian)
`MixedGaussianTemplate()`	Create a template MixedGaussian object containing a regime for each model type
`PCM()`	Create a phylogenetic comparative model object
`PCMAbCdEf()`	Quadratic polynomial parameters A, b, C, d, E, f for each node
`PCMAddToListAttribute()`	Add a value to a list-valued attribute of a member or members matching a pattern
`PCMApplyTransformation()`	Map a parametrization to its original form.
`PCMBaseIsADevRelease()`	Check if the PCMBase version corresponds to a dev release
`PCMBaseTestObjects`	Test objects for the PCMBase package
`PCMColorPalette()`	A fixed palette of n colors
`PCMCombineListAttribute()`	Combine all member attributes of a given name into a list
`PCMCond(<GaussianPCM>)`	Conditional distribution of a daughter node given its parent node
`PCMCond()`	Conditional distribution of a daughter node given its parent node
`PCMCondVOU()`	Variance-covariance matrix of an OU process with optional measurement error and jump at the start
`PCMCreateLikelihood()`	Create a likelihood function of a numerical vector parameter
`PCMDefaultModelTypes()` `MGPMDefaultModelTypes()`	Class names for the the default PCM and MGPM model types
`PCMDefaultObject()`	Generate a default object of a given PCM model type or parameter type
`PCMDescribe()`	Human friendly description of a PCM
`PCMDescribeParameters()`	Describe the parameters of a PCM
`PCMExtractDimensions()`	Given a PCM or a parameter object, extract an analogical object for a subset of the dimensions (traits) in the original object.
`PCMExtractRegimes()`	Given a PCM or a parameter object, extract an analogical object for a subset of the regimes in the original object.
`PCMFindMethod()`	Find the S3 method for a given PCM object or class-name and an S3 generic
`PCMFixParameter()`	Fix a parameter in a PCM model
`PCMGenerateModelTypes()`	Generate default model types for given PCM base-classes
`PCMGenerateParameterizations()`	Generate possible parameterizations for a given type of model
`PCMGetAttribute()`	Value of an attribute of an object or values for an attribute found in its members
`PCMGetVecParamsRegimesAndModels()`	Get a vector of all parameters (real and discrete) describing a model on a tree including the numerical parameters of each model regime, the integer ids of the splitting nodes defining the regimes on the tree and the integer ids of the model types associated with each regime.
`PCMInfo()`	Meta-information about a tree and trait data associated with a PCM
`PCMLik()`	Likelihood of a multivariate Gaussian phylogenetic comparative model with non-interacting lineages
`PCMLikDmvNorm()`	Calculate the likelihood of a model using the standard formula for multivariate pdf
`PCMLikTrace()`	Tracing the log-likelihood calculation of a model over each node of the tree
`PCMListMembers()`	A vector of access-code strings to all members of a named list
`PCMListParameterizations()` `PCMListDefaultParameterizations()`	Specify the parameterizations for each parameter of a model
`PCMLmr()`	Quadratic polynomial parameters L, m, r
`PCMMapModelTypesToRegimes()`	Integer vector giving the model type index for each regime
`PCMMean()`	Expected mean vector at each tip conditioned on a trait-value vector at the root
`PCMMeanAtTime()`	Calculate the mean at time t, given X0, under a PCM model
`PCMModels()`	Get a list of PCM models currently implemented
`PCMModelTypes()`	Get the model type(s) of a model
`PCMNumRegimes()`	Number of regimes in a obj
`PCMNumTraits()`	Number of traits modeled by a PCM
`PCMOptions()`	Global options for the PCMBase package
`PCMPairSums()`	Sums of pairs of elements in a vector
`PCMParam`	Module PCMParam
`PCMParamCount()`	Count the number of free parameters associated with a PCM or a PCM-parameter
`PCMParamGetShortVector()`	Get a vector of the variable numeric parameters in a model
`PCMParamLoadOrStore()`	Load (or store) a PCM parameter from (or to) a vector of the variable parameters in a model.
`PCMParamLocateInShortVector()`	Locate a named parameter in the short vector representation of a model
`PCMParamLowerLimit()`	The lower limit for a given model or parameter type
`PCMParamRandomVecParams()`	Generate a random parameter vector for a model using uniform distribution between its lower and upper bounds.
`PCMParamSetByName()`	Set model parameters from a named list
`is.Local()` `is.Global()` `is.ScalarParameter()` `is.VectorParameter()` `is.MatrixParameter()` `is.WithCustomVecParams()` `is.Fixed()` `is.Zeros()` `is.Ones()` `is.Identity()` `is.AllEqual()` `is.NonNegative()` `is.Diagonal()` `is.ScalarDiagonal()` `is.Symmetric()` `is.UpperTriangular()` `is.UpperTriangularWithDiagonal()` `is.WithNonNegativeDiagonal()` `is.LowerTriangular()` `is.LowerTriangularWithDiagonal()` `is.Omitted()` `is.CholeskyFactor()` `is.Schur()` `is.Transformable()` `is.Transformed()` `is.SemiPositiveDefinite()`	Parameter types
`PCMParamUpperLimit()`	The upper limit for a given model or parameter type
`PCMParentClasses()`	Parent S3 classes for a model class
`PCMParseErrorMessage()`	Extract error information from a formatted error message.
`PCMPExpxMeanExp()`	Create a function of time that calculates (1-exp(-lambda_ij*time))/lambda_ij for every element lambda_ij of the input matrix Lambda_ij.
`PCMPLambdaP_1()`	Eigen-decomposition of a matrix H
`PCMPlotGaussianDensityGrid2D()`	A 2D Gaussian distribution density grid in the form of a ggplot object
`PCMPlotGaussianSample2D()`	A 2D sample from Gaussian distribution
`PCMPlotMath()`	Beautiful model description based on plotmath
`PCMPlotTraitData2D()`	Scatter plot of 2-dimensional data
`PCMPresentCoordinates()`	Determine which traits are present (active) on each node of the tree
`PCMRegimes()`	Get the regimes (aka colors) of a PCM or of a PCMTree object
`PCMSetAttribute()`	Set an attribute of a named member in a PCM or other named list object
`PCMSim()`	Simulation of a phylogenetic comparative model on a tree
`PCMSpecify()`	Parameter specification of PCM model
`PCMTable()`	A data.table representation of a PCM object
`PCMTableParameterizations()`	Cartesian product of possible parameterizations for the different parameters of a model
`PCMTrajectory()`	Generate a trajectory for the mean in one regime of a PCM
`PCMTree()`	Create a PCMTree object from a phylo object
`PCMTreeBackbonePartition()`	Prune the tree leaving one tip for each or some of its parts
`PCMTreeDropClade()`	Drop a clade from a phylogenetic tree
`PCMTreeDtNodes()`	A data.table with time, part and regime information for the nodes in a tree
`PCMTreeEdgeTimes()`	A matrix with the begin and end time from the root for each edge in tree
`PCMTreeEvalNestedEDxOnTree()`	Perfrorm nested extractions or drops of clades from a tree
`PCMTreeExtractClade()`	Extract a clade from phylogenetic tree
`PCMTreeGetBranchLength()`	The length of the branch leading to a node
`PCMTreeGetDaughters()`	A vector of the daughter nodes for a given parent node id in a tree
`PCMTreeGetLabels()` `PCMTreeGetRootLabel()` `PCMTreeGetNodeLabels()` `PCMTreeGetTipLabels()`	Node labels of a tree
`PCMTreeGetParent()`	The parent node id of a daughter node in a tree
`PCMTreeGetPartition()`	Get the starting branch' nodes for each part on a tree
`PCMTreeGetPartNames()`	Unique parts on a tree in the order of occurrence from the root to the tips (preorder)
`PCMTreeGetPartRegimes()`	Regime mapping for the parts in a tree
`PCMTreeGetPartsForNodes()`	Get the parts of the branches leading to a set of nodes or tips
`PCMTreeGetRegimesForEdges()`	Model regimes (i.e. colors) associated with the branches in a tree
`PCMTreeGetRegimesForNodes()`	Get the regimes of the branches leading to a set of nodes or tips
`PCMTreeGetTipsInPart()`	Get the tips belonging to a part in a tree
`PCMTreeGetTipsInRegime()`	Get the tips belonging to a regime in a tree
`PCMTreeInsertSingletons()` `PCMTreeInsertSingletonsAtEpoch()` `PCMTreeInsertTipsOrSingletons()`	Insert tips or singleton nodes on chosen edges
`PCMTreeJumps()`	Jumps in modeled traits associated with branches in a tree
`PCMTreeListAllPartitions()`	A list of all possible (including recursive) partitions of a tree
`PCMTreeListCladePartitions()`	A list of all possible clade partitions of a tree with a number of splitting nodes
`PCMTreeListDescendants()`	A list of the descendants for each node in a tree
`PCMTreeListRootPaths()`	A list of the path to the root from each node in a tree
`PCMTreeLocateEpochOnBranches()`	Find the crossing points of an epoch-time with each lineage of a tree
`PCMTreeLocateMidpointsOnBranches()`	Find the middle point of each branch longer than a threshold
`PCMTreeMatchLabels()`	Get the node numbers associated with tip- or node-labels in a tree
`PCMTreeMatrixNodesInSamePart()` `PCMTreeMatrixNodesInSameRegime()`	Which couples from a given set of nodes in a tree belong to the same part?
`PCMTreeNearestNodesToEpoch()`	Find the nearest node to a given time from the root (epoch) on each lineage crossing this epoch
`PCMTreeNodeTimes()`	Calculate the time from the root to each node of the tree
`PCMTreeNumNodes()`	Number of all nodes in a tree
`PCMTreeNumParts()`	Number of unique parts on a tree
`PCMTreeNumTips()`	Wrapper for length(tree$tip.label)
`PCMTreePlot()`	Plot a tree with parts and regimes assigned to these parts
`PCMTreePostorder()`	Post-order tree traversal
`PCMTreePreorder()`	Pre-order tree traversal
`PCMTreeSetLabels()`	Set tip and internal node labels in a tree
`PCMTreeSetPartition()`	Set a partition of a tree by specifying the partition nodes
`PCMTreeSetPartRegimes()`	Set regimes for the parts in a tree
`PCMTreeSetRegimesForEdges()`	Set the regime for each individual edge in a tree explicitly
`PCMTreeSplitAtNode()`	Slit a tree at a given internal node into a clade rooted at this node and the remaining tree after dropping this clade
`PCMTreeTableAncestors()`	A matrix (table) of ancestors/descendants for each node in a tree
`PCMTreeToString()`	A character representation of a phylo object.
`PCMTreeVCV()`	Phylogenetic Variance-covariance matrix
`PCMUnfixParameter()`	Unfix a parameter in a PCM model
`PCMVar()`	Expected variance-covariance matrix for each couple of tips (i,j)
`PCMVarAtTime()`	Calculate the variance covariance k x k matrix at time t, under a PCM model
`TruePositiveRate()` `FalsePositiveRate()`	True positive rate of a set of binary predictions against their trues
`UpperTriFactor()`	Upper triangular factor of a symmetric positive definite matrix
`White`	White Gaussian PCM ignoring phylogenetic history

Reference

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