PCMCreateLikelihood

a <code>k x N</code> numerical matrix with possible <code>NA</code> and <code>NaN</code> entries. Each
column of X contains the measured trait values for one species (tip in tree).
Missing values can be either not-available (<code>NA</code>) or not existing (<code>NaN</code>).
These two values have are treated differently when calculating
likelihoods: see <code><a rd-options="" href="/link/PCMPresentCoordinates?package=PCMBase&version=1.2.10" data-mini-rdoc="PCMBase::PCMPresentCoordinates">PCMPresentCoordinates</a></code>.

tree

an S3 object specifying both, the model type (class, e.g. "OU") as
well as the concrete model parameter values at which the likelihood is to be
calculated (see also Details).

model

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>.

a list returned from a call to <code>PCMInfo(X, tree, model, SE)</code>,
containing meta-data such as N, M and k. Alternatively, this can be a
function object that returns such a list, e.g. the function<code>PCMInfo</code>
or the function <code>PCMInfoCpp</code> from the <code>PCMBaseCpp</code> package.

metaI

positive numerical value (default Inf), which
serves as a guard for numerical error. Values exceeding
this positiveGuard are most likely due to numerical error and
PCMOptions()$PCMBase.Value.NA is returned instead.

positiveValueGuard

Create a likelihood function of a numerical vector parameter

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 ML and Bayesian fit 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

PCMCreateLikelihood function

a <code>k x N</code> numerical matrix with possible <code>NA</code> and <code>NaN</code> entries. Each
column of X contains the measured trait values for one species (tip in tree).
Missing values can be either not-available (<code>NA</code>) or not existing (<code>NaN</code>).
These two values have are treated differently when calculating
likelihoods: see <code><a rd-options='' href='PCMPresentCoordinates'>PCMPresentCoordinates</a></code>.

PCMCreateLikelihood: Create a likelihood function of a numerical vector parameter

Description

Usage

Arguments

Value

Details