PCMTreePlot

Plot a tree with parts and regimes assigned to these parts

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

PCMTreePlot function

<dl><dt>tree</dt>
<dd>a PCMTree or a phylo object.</dd>
<dt>palette</dt>
<dd>a named vector of colors corresponding to the regimes in tree</dd>
<dt>...</dt>
<dd>Arguments passed to ggtree, e.g. layout = 'fan', open.angle = 8,
size=.25.</dd></dl>

Arguments

Plot a tree with parts and regimes assigned to these parts — PCMTreePlot

<dl>

<dt>tree</dt>
<dd>a PCMTree or a phylo object.</dd>


<dt>palette</dt>
<dd>a named vector of colors corresponding to the regimes in tree</dd>


<dt>...</dt>
<dd>Arguments passed to ggtree, e.g. layout = 'fan', open.angle = 8,
size=.25.</dd>

</dl>

PCMTreePlot: Plot a tree with parts and regimes assigned to these parts

Description

Usage

Arguments