Simulation and Likelihood Calculation of Phylogenetic Comparative Models
Arguments to be passed to the constructor MixedGaussian when construct...
Arguments for the MixedGaussian constructor for scalar OU MGPM models.
Arguments for the MixedGaussian constructor for SURFACE OU MGPM models...
Convert a GaussianPCM model object to a MixedGaussian model object
Latex representation of a model parameter or other found in a data.tab...
Latex representation of a data.table with matrix and vectors in its ce...
Check if an object is a GaussianPCM
Check if an object is a MixedGaussian PCM
Check if an object is a PCM.
Check that a tree is a PCMTree
Find the members in a list matching a member expression
Class name for the scalar OU MGPM model type
Class name for the SURFACE OU MGPM model type
Create a multi-regime Gaussian model (MixedGaussian)
Create a template MixedGaussian object containing a regime for each mo...
Create a phylogenetic comparative model object
Quadratic polynomial parameters A, b, C, d, E, f for each node
Add a value to a list-valued attribute of a member or members matching...
Map a parametrization to its original form.
Check if the PCMBase version corresponds to a dev release
A fixed palette of n colors
Combine all member attributes of a given name into a list
Conditional distribution of a daughter node given its parent node
Conditional distribution of a daughter node given its parent node
Variance-covariance matrix of an OU process with optional measurement ...
Create a likelihood function of a numerical vector parameter
Class names for the the default PCM and MGPM model types
Generate a default object of a given PCM model type or parameter type
Human friendly description of a PCM
Describe the parameters of a PCM
Given a PCM or a parameter object, extract an analogical object for a ...
Given a PCM or a parameter object, extract an analogical object for a ...
Find the S3 method for a given PCM object or class-name and an S3 gene...
Fix a parameter in a PCM model
Generate default model types for given PCM base-classes
Generate possible parameterizations for a given type of model
Value of an attribute of an object or values for an attribute found in...
Get a vector of all parameters (real and discrete) describing a model ...
Meta-information about a tree and trait data associated with a PCM
Likelihood of a multivariate Gaussian phylogenetic comparative model w...
Calculate the likelihood of a model using the standard formula for mul...
Tracing the log-likelihood calculation of a model over each node of th...
A vector of access-code strings to all members of a named list
Specify the parameterizations for each parameter of a model
Quadratic polynomial parameters L, m, r
Integer vector giving the model type index for each regime
Expected mean vector at each tip conditioned on a trait-value vector a...
Calculate the mean at time t, given X0, under a PCM model
Get a list of PCM models currently implemented
Get the model type(s) of a model
Number of regimes in a obj
Number of traits modeled by a PCM
Global options for the PCMBase package
Sums of pairs of elements in a vector
Module PCMParam
Bind named vectors or matrices into an array so that the names form th...
Count the number of free parameters associated with a PCM or a PCM-par...
Get a vector of the variable numeric parameters in a model
Load (or store) a PCM parameter from (or to) a vector of the variable ...
Locate a named parameter in the short vector representation of a model
The lower limit for a given model or parameter type
Generate a random parameter vector for a model using uniform distribut...
Set model parameters from a named list
Parameter types
The upper limit for a given model or parameter type
Parent S3 classes for a model class
Extract error information from a formatted error message.
Create a function of time that calculates $(1-exp(-lambda_ij*time))/la...
Eigen-decomposition of a matrix H
A 2D Gaussian distribution density grid in the form of a ggplot object
A 2D sample from Gaussian distribution
Beautiful model description based on plotmath
Scatter plot of 2-dimensional data
Determine which traits are present (active) on each node of the tree
Get the regimes (aka colors) of a PCM or of a PCMTree object
Set an attribute of a named member in a PCM or other named list object
Simulation of a phylogenetic comparative model on a tree
Parameter specification of PCM model
A data.table representation of a PCM object
Cartesian product of possible parameterizations for the different para...
Generate a trajectory for the mean in one regime of a PCM
Create a PCMTree object from a phylo object
Prune the tree leaving one tip for each or some of its parts
Drop a clade from a phylogenetic tree
A data.table with time, part and regime information for the nodes in a...
A matrix with the begin and end time from the root for each edge in tr...
Perfrorm nested extractions or drops of clades from a tree
Extract a clade from phylogenetic tree
The length of the branch leading to a node
A vector of the daughter nodes for a given parent node id in a tree
Node labels of a tree
The parent node id of a daughter node in a tree
Get the starting branch' nodes for each part on a tree
Unique parts on a tree in the order of occurrence from the root to the...
Regime mapping for the parts in a tree
Get the parts of the branches leading to a set of nodes or tips
Model regimes (i.e. colors) associated with the branches in a tree
Get the regimes of the branches leading to a set of nodes or tips
Get the tips belonging to a part in a tree
Get the tips belonging to a regime in a tree
Insert tips or singleton nodes on chosen edges
Jumps in modeled traits associated with branches in a tree
A list of all possible (including recursive) partitions of a tree
A list of all possible clade partitions of a tree with a number of spl...
A list of the descendants for each node in a tree
A list of the path to the root from each node in a tree
Find the crossing points of an epoch-time with each lineage of a tree
Find the middle point of each branch longer than a threshold
Get the node numbers associated with tip- or node-labels in a tree
Which couples from a given set of nodes in a tree belong to the same p...
Find the nearest node to a given time from the root (epoch) on each li...
Calculate the time from the root to each node of the tree
Number of all nodes in a tree
Number of unique parts on a tree
Wrapper for length(tree$tip.label)
Plot a tree with parts and regimes assigned to these parts
Post-order tree traversal
Pre-order tree traversal
Set tip and internal node labels in a tree
Set a partition of a tree by specifying the partition nodes
Set regimes for the parts in a tree
Set the regime for each individual edge in a tree explicitly
Slit a tree at a given internal node into a clade rooted at this node ...
A matrix (table) of ancestors/descendants for each node in a tree
A character representation of a phylo object.
Phylogenetic Variance-covariance matrix
Unfix a parameter in a PCM model
Expected variance-covariance matrix for each couple of tips (i,j)
Calculate the variance covariance k x k matrix at time t, under a PCM ...
Check if all packages listed in Suggests are available
True positive rate of a set of binary predictions against their trues
Upper triangular factor of a symmetric positive definite matrix
White Gaussian PCM ignoring phylogenetic history
Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for inference of these models to tree and trait data. The package web-site <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.
Useful links