| Args_MixedGaussian_MGPMDefaultModelTypes | Arguments to be passed to the constructor MixedGaussian when... |
| Args_MixedGaussian_MGPMScalarOUType | Arguments for the MixedGaussian constructor for scalar OU... |
| Args_MixedGaussian_MGPMSurfaceOUType | Arguments for the MixedGaussian constructor for SURFACE OU... |
| as.MixedGaussian | Convert a 'GaussianPCM' model object to a 'MixedGaussian'... |
| dataFig3 | Data for Fig3 in the TPB manuscript |
| FormatCellAsLatex | Latex representation of a model parameter or other found in a... |
| FormatTableAsLatex | Latex representation of a data.table with matrix and vectors... |
| 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... |
| PCM | Create a phylogenetic comparative model object |
| PCMAbCdEf | Quadratic polynomial parameters A, b, C, d, E, f for each... |
| PCMAddToListAttribute | Add a value to a list-valued attribute of a member or members... |
| 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... |
| PCMCond.GaussianPCM | Conditional distribution of a daughter node given its parent... |
| PCMCondVOU | Variance-covariance matrix of an OU process with optional... |
| 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... |
| 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... |
| PCMExtractRegimes | Given a PCM or a parameter object, extract an analogical... |
| PCMFindMethod | Find the S3 method for a given PCM object or class-name and... |
| 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... |
| PCMGetVecParamsRegimesAndModels | Get a vector of all parameters (real and discrete) describing... |
| PCMInfo | Meta-information about a tree and trait data associated with... |
| PCMLik | Likelihood of a multivariate Gaussian phylogenetic... |
| PCMLikDmvNorm | Calculate the likelihood of a model using the standard... |
| PCMLikTrace | Tracing the log-likelihood calculation of a model over each... |
| PCMListMembers | A vector of access-code strings to all members of a named... |
| 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... |
| 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... |
| 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... |
| PCMParamLocateInShortVector | Locate a named parameter in the short vector representation... |
| PCMParamLowerLimit | The lower limit for a given model or parameter type |
| PCMParamRandomVecParams | Generate a random parameter vector for a model using uniform... |
| 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. |
| PCMPExpxMeanExp | Create a function of time that calculates... |
| PCMPLambdaP_1 | Eigen-decomposition of a matrix H |
| PCMPlotGaussianDensityGrid2D | A 2D Gaussian distribution density grid in the form of a... |
| 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... |
| 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... |
| 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... |
| 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... |
| PCMTreeEdgeTimes | A matrix with the begin and end time from the root for each... |
| 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... |
| PCMTreeGetLabels | 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... |
| PCMTreeGetPartRegimes | Regime mapping for the parts in a tree |
| PCMTreeGetPartsForNodes | Get the parts of the branches leading to a set of nodes or... |
| PCMTreeGetRegimesForEdges | Model regimes (i.e. colors) associated with the branches in a... |
| PCMTreeGetRegimesForNodes | Get the regimes of the branches leading to a set of nodes or... |
| 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... |
| PCMTreeListCladePartitions | A list of all possible clade partitions of a tree with a... |
| 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... |
| 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... |
| PCMTreeMatrixNodesInSamePart | Which couples from a given set of nodes in a tree belong to... |
| PCMTreeNearestNodesToEpoch | Find the nearest node to a given time from the root (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... |
| PCMTreeTableAncestors | A matrix (table) of ancestors/descendants for each node in a... |
| 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... |
| PCMVarAtTime | Calculate the variance covariance k x k matrix at time t,... |
| RequireSuggestedPackages | Check if all packages listed in Suggests are available |
| TruePositiveRate | True positive rate of a set of binary predictions against... |
| UpperTriFactor | Upper triangular factor of a symmetric positive definite... |
| White | White Gaussian PCM ignoring phylogenetic history |
