## 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.

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(<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

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

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.

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

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() PCMTreeInsertSingletonsAtEpoch()

Insert 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

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

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

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