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.
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
MGPMScalarOUType        Class name for the scalar OU MGPM model type
MGPMSurfaceOUType       Class name for the SURFACE OU MGPM model type
MatchListMembers        Find the members in a list matching a member
                        expression
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                 Conditional distribution of a daughter node
                        given its parent node
PCMCond.GaussianPCM     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    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
                        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
PCMModelTypes           Get the model type(s) of a model
PCMModels               Get a list of PCM models currently implemented
PCMNumRegimes           Number of regimes in a obj
PCMNumTraits            Number of traits modeled by a PCM
PCMOptions              Global options for the PCMBase package
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
PCMPairSums             Sums of pairs of elements in a vector
PCMParam                Module PCMParam
PCMParamBindRegimeParams
                        Bind named vectors or matrices into an array so
                        that the names form the names of the last
                        dimension.
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
PCMParamType            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.
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        Node labels of a tree
PCMTreeGetParent        The parent node id of a daughter node in 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
PCMTreeGetPartition     Get the starting branch' nodes for each part on
                        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
                        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
                        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
PCMTreeSetPartRegimes   Set regimes for the parts in a tree
PCMTreeSetPartition     Set a partition of a tree by specifying the
                        partition nodes
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
RequireSuggestedPackages
                        Check if all packages listed in Suggests are
                        available
TruePositiveRate        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
as.MixedGaussian        Convert a 'GaussianPCM' model object to a
                        'MixedGaussian' model object
dataFig3                Data for Fig3 in the TPB manuscript
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
