sim.rates

multiOU

is a stochastic map format phylogenetic tree in modified <code>"phylo"</code> format (e.g., see <code><a rd-options="" href="/link/make.simmap?package=phytools&version=1.0-3" data-mini-rdoc="phytools::make.simmap">make.simmap</a></code>).

tree

a named vector containing the rates for each state; names should be states in <code>mtree</code>.

sig2

optional value for the root state.

nsim

logical value indicating whether to return states at internal nodes.

internal

logical value indicating whether or not to visual the rate heterogeneity (default value is <code>FALSE</code>.

plot

single value or vector of values of the OU \(\alpha\) parameter.

alpha

single value or vector of values of the OU \(\theta\) parameter.

theta

optional value of the root state. Defaults to zero.

The function <code>sim.rates</code> conducts BM simulation on a tree with multiple rates.	
The function <code>multiOU</code> conducts multi-regime OU simulations on the tree under a range of conditions.

Simulation

phylogenetics

comparative method

continuous character

A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

sim.rates function

<dl>	<dt>tree</dt>
<dd>is a stochastic map format phylogenetic tree in modified <code>"phylo"</code> format (e.g., see <code>make.simmap</code>).</dd>	<dt>sig2</dt>
<dd>a named vector containing the rates for each state; names should be states in <code>mtree</code>.</dd>	<dt>anc</dt>
<dd>optional value for the root state.</dd>	<dt>nsim</dt>
<dd>number of simulations.</dd>	<dt>internal</dt>
<dd>logical value indicating whether to return states at internal nodes.</dd>	<dt>plot</dt>
<dd>logical value indicating whether or not to visual the rate heterogeneity (default value is <code>FALSE</code>.</dd>	<dt>alpha</dt>
<dd>single value or vector of values of the OU \(\alpha\) parameter.</dd>	<dt>theta</dt>
<dd>single value or vector of values of the OU \(\theta\) parameter.</dd>	<dt>a0</dt>
<dd>optional value of the root state. Defaults to zero.</dd>	<dt>...</dt>
<dd>optional arguments.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.0-3" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Brownian or OU simulation with multiple evolutionary regimes — sim.rates

<dl>

	<dt>tree</dt>
<dd>is a stochastic map format phylogenetic tree in modified <code>"phylo"</code> format (e.g., see <code>make.simmap</code>).</dd>

	<dt>sig2</dt>
<dd>a named vector containing the rates for each state; names should be states in <code>mtree</code>.</dd>

	<dt>anc</dt>
<dd>optional value for the root state.</dd>

	<dt>nsim</dt>
<dd>number of simulations.</dd>

	<dt>internal</dt>
<dd>logical value indicating whether to return states at internal nodes.</dd>

	<dt>plot</dt>
<dd>logical value indicating whether or not to visual the rate heterogeneity (default value is <code>FALSE</code>.</dd>

	<dt>alpha</dt>
<dd>single value or vector of values of the OU \(\alpha\) parameter.</dd>

	<dt>theta</dt>
<dd>single value or vector of values of the OU \(\theta\) parameter.</dd>

	<dt>a0</dt>
<dd>optional value of the root state. Defaults to zero.</dd>

	<dt>...</dt>
<dd>optional arguments.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

sim.rates: Brownian or OU simulation with multiple evolutionary regimes

Description

Usage

Value

Arguments

Author

Details

References

See Also