All functions

MixedGaussian()

Create a multi-regime Gaussian model (MixedGaussian)

PCM()

Create a phylogenetic comparative model object

PCMAbCdEf()

Quadratic polynomial parameters A, b, C, d, E, f for each node

PCMApplyTransformation()

Map a parametrization to its original form.

PCMBaseIsADevRelease()

Check if the PCMBase version correpsonds to a dev release

PCMColorPalette()

A fixed palette of n colors

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 likelhood function of a numerical vector parameter

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

PCMFixParameter()

Fix a parameter in a PCM model

PCMGenerateParameterizations()

Generate possible parameterizations for a given type of model

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 spliting nodes defining the regimes on the tree and the integer ids of the model classes associated with each regime.

PCMInfo()

Meta-information about a tree associated with a PCM

PCMLik()

Likelihood of a multivariate Gaussian phylogenetic comparative model with non-interacting lineages

PCMListParameterizations()

Specify the parameterizations for each parameter of a model

PCMLmr()

Quadratic polynomial parameters L, m, r

PCMMapModelTypesToRegimes()

#' Regimes in a model #' @param model a PCM object #' @param tree a phylo object or NULL. If the regimes in the model are integers and tree is not NULL, #' then these integers are used as indexes in PCMTreeUniqueRegimes(tree). Default NULL. #' @return a character or an integer vector giving the regime names of the models #' @export PCMRegimes <- function(model, tree = NULL, preorder = if(is.null(tree)) NULL else PCMTreePreorder(tree)) UseMethod("PCMRegimes", model)

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

PCMNumRegimes()

Number of regimes in a model

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.

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.CholeskiFactor() 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()

Regimes in a model

PCMSim()

Simulation of a phylogenetic comparative model on a tree

PCMSpecify()

Parameter specification of PCM model

PCMTableParameterizations()

Cartesian product of possible parameterizations for the different parameters of a model

PCMTreeDropClade()

Drop a clade from a phylogenetic tree

PCMTreeDtNodeRegimes()

A data.table of the tips with their assigned regime

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

PCMTreeExtractBackboneRegimes()

Prune the tree leaving one tip for each regime

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()

Get a vector of the tip and node labels in a tree

PCMTreeGetParent()

The parent node id of a daughter node in a tree

PCMTreeGetRegimeForNode()

Get the regime of the branch leading to a node or a tip

PCMTreeGetStartingNodesRegimes()

Get the starting branch' nodes for each regime on a tree

PCMTreeGetTipsInRegime()

Get the tips belonging to a regime tree

PCMTreeInsertSingletons() PCMTreeInsertSingletonsAtEpoch()

Insert singleton nodes on chosen edges

PCMTreeJumps()

Jumps in modeled traits associated with branches in a tree

PCMTreeListCladePartitions()

A list of all possible 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

PCMTreeMatchRegimesWithModel()

Regimes associated with branches in a tree

PCMTreeMatrixNodesInSameRegime()

Which nodes in a tree belong to the same regime?

PCMTreeMatrixTipsInSameRegime()

Which tips in a tree belong to the same regime?

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

PCMTreeNumTips()

Wrapper for length(tree$tip.label)

PCMTreeNumUniqueRegimes()

Number of unique regimes on a tree

PCMTreePlot()

Plot a tree with regimes

PCMTreePostorder()

Post-order tree traversal

PCMTreePreorder()

Pre-order tree traversal

PCMTreeSetDefaultRegime()

Set a default edge.regime member ot the passed tree object

PCMTreeSetLabels()

Set tip and internal node labels in a tree

PCMTreeSetRegimes()

Assign regimes on a tree given a set of starting branches

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.

PCMTreeUniqueRegimes()

Unique regimes on a tree in the order of occurrence from the root to the tips (preorder)

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

White

White Gaussian PCM ignoring phylogenetic history

is.MixedGaussian()

Check if an object is a `MixedGaussian` PCM

is.PCM()

Check if an object is a PCM.