PCMSim

Generate trait data on a tree according to a multivariate stochastic
model with one or several regimes

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.

Venelin Mitov

PCMBase

Simulation and Likelihood Calculation of Phylogenetic
Comparative Models

Krzysztof Bartoszek

Georgios Asimomitis

Tanja Stadler

PCMSim function

<dl><dt>tree</dt>
<dd>a phylo object specifying a rooted tree.</dd>
<dt>model</dt>
<dd>an S3 object specifying the model (see Details).</dd>
<dt>X0</dt>
<dd>a numeric vector of length k (the number of traits) specifying the
trait values at the root of the tree.</dd>
<dt>SE</dt>
<dd>a k x N matrix specifying the standard error for each measurement in
X. Alternatively, a k x k x N cube specifying an upper triangular k x k
factor of the variance covariance matrix for the measurement error
for each node i=1, ..., N.
Default: <code>matrix(0.0, PCMNumTraits(model), PCMTreeNumTips(tree))</code>.</dd>
<dt>metaI</dt>
<dd>a named list containing meta-information about the data and the
model.</dd>
<dt>verbose</dt>
<dd>a logical indicating if informative messages should be written
during execution.</dd></dl>

Arguments

Simulation of a phylogenetic comparative model on a tree — PCMSim

<dl>

<dt>tree</dt>
<dd>a phylo object specifying a rooted tree.</dd>


<dt>model</dt>
<dd>an S3 object specifying the model (see Details).</dd>


<dt>X0</dt>
<dd>a numeric vector of length k (the number of traits) specifying the
trait values at the root of the tree.</dd>


<dt>SE</dt>
<dd>a k x N matrix specifying the standard error for each measurement in
X. Alternatively, a k x k x N cube specifying an upper triangular k x k
factor of the variance covariance matrix for the measurement error
for each node i=1, ..., N.
Default: <code>matrix(0.0, PCMNumTraits(model), PCMTreeNumTips(tree))</code>.</dd>


<dt>metaI</dt>
<dd>a named list containing meta-information about the data and the
model.</dd>


<dt>verbose</dt>
<dd>a logical indicating if informative messages should be written
during execution.</dd>

</dl>

PCMSim: Simulation of a phylogenetic comparative model on a tree

Description

Usage

Value

Arguments

Details

See Also

Examples