PCMPExpxMeanExp

Create a function of time that calculates \((1-exp(-lambda_ij*time))/lambda_ij\)
for every element \(lambda_ij\) of the input matrix \(Lambda_ij\).

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

PCMPExpxMeanExp function

<dl><dt>Lambda_ij</dt>
<dd>a squared numerical matrix of dimension k x k</dd>
<dt>threshold.Lambda_ij</dt>
<dd>a 0-threshold for abs(Lambda_i + Lambda_j), where Lambda_i
and Lambda_j are eigenvalues of the parameter matrix H. This
threshold-value is used as a condition to
take the limit time of the expression `(1-exp(-Lambda_ij*time))/Lambda_ij` as
`(Lambda_i+Lambda_j) --&gt; 0`. You can control this value by the global option
"PCMBase.Threshold.Lambda_ij". The default value (1e-8) is suitable for branch
 lengths bigger than 1e-6. For smaller branch lengths, you may want to
 increase the threshold value using, e.g.
`options(PCMBase.Threshold.Lambda_ij=1e-6)`.</dd></dl>

Arguments

Create a function of time that calculates \((1-exp(-lambda_ij*time))/lambda_ij\)
for every element \(lambda_ij\) of the input matrix \(Lambda_ij\). — PCMPExpxMeanExp

<dl>

<dt>Lambda_ij</dt>
<dd>a squared numerical matrix of dimension k x k</dd>


<dt>threshold.Lambda_ij</dt>
<dd>a 0-threshold for abs(Lambda_i + Lambda_j), where Lambda_i
and Lambda_j are eigenvalues of the parameter matrix H. This
threshold-value is used as a condition to
take the limit time of the expression `(1-exp(-Lambda_ij*time))/Lambda_ij` as
`(Lambda_i+Lambda_j) --&gt; 0`. You can control this value by the global option
"PCMBase.Threshold.Lambda_ij". The default value (1e-8) is suitable for branch
 lengths bigger than 1e-6. For smaller branch lengths, you may want to
 increase the threshold value using, e.g.
`options(PCMBase.Threshold.Lambda_ij=1e-6)`.</dd>

</dl>

PCMPExpxMeanExp: Create a function of time that calculates \((1-exp(-lambda_ij*time))/lambda_ij\) for every element \(lambda_ij\) of the input matrix \(Lambda_ij\).

Description

Usage

Value

Arguments

Details