Simulation and Likelihood Calculation of Phylogenetic Comparative Models

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... |

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.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) |

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 | Get a vector of the tip and node labels in 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 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,... |

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 |

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