fastBM

is a phylogenetic tree in <code>"phylo"</code> format.

tree

a value for ancestral state at the root node.

an optional value for the mean of random normal changes along branches of the tree - can be used to simulate a trend if <code>mu!=0</code>.

instantaneous variance of the BM process, \(\sigma^2\).

sig2

a vector with the lower and upper bounds (respectively) for bounded Brownian simulation - by default simulation is unbounded.

bounds

logical value indicating whether or not to return states for internal nodes.

internal

nsim

optional arguments <code>alpha</code> and <code>theta</code> used for OU simulation. If <code>alpha</code> is set then <code>mu</code> and <code>bounds</code> are ignored with a warning.

This function conducts (reasonably) fast quantitative trait simulation on a phylogeny under several different models: Brownian motion (default), BM with a trend (for <code>mu!=0</code>), bounds (for <code>bounds!=c(-Inf,</code> <code>Inf)</code>), and OU.

Simulation

phylogenetics

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)

fastBM function

<dl>	<dt>tree</dt>
<dd>is a phylogenetic tree in <code>"phylo"</code> format.</dd>	<dt>a</dt>
<dd>a value for ancestral state at the root node.</dd>	<dt>mu</dt>
<dd>an optional value for the mean of random normal changes along branches of the tree - can be used to simulate a trend if <code>mu!=0</code>.</dd>	<dt>sig2</dt>
<dd>instantaneous variance of the BM process, \(\sigma^2\).</dd>	<dt>bounds</dt>
<dd>a vector with the lower and upper bounds (respectively) for bounded Brownian simulation - by default simulation is unbounded.</dd>	<dt>internal</dt>
<dd>logical value indicating whether or not to return states for internal nodes.</dd>	<dt>nsim</dt>
<dd>number of simulations.</dd>	<dt>...</dt>
<dd>optional arguments <code>alpha</code> and <code>theta</code> used for OU simulation. If <code>alpha</code> is set then <code>mu</code> and <code>bounds</code> are ignored with a warning.</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

(Reasonably) fast quantitative trait simulation on phylogenies — fastBM

<dl>

	<dt>tree</dt>
<dd>is a phylogenetic tree in <code>"phylo"</code> format.</dd>

	<dt>a</dt>
<dd>a value for ancestral state at the root node.</dd>

	<dt>mu</dt>
<dd>an optional value for the mean of random normal changes along branches of the tree - can be used to simulate a trend if <code>mu!=0</code>.</dd>

	<dt>sig2</dt>
<dd>instantaneous variance of the BM process, \(\sigma^2\).</dd>

	<dt>bounds</dt>
<dd>a vector with the lower and upper bounds (respectively) for bounded Brownian simulation - by default simulation is unbounded.</dd>

	<dt>internal</dt>
<dd>logical value indicating whether or not to return states for internal nodes.</dd>

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

	<dt>...</dt>
<dd>optional arguments <code>alpha</code> and <code>theta</code> used for OU simulation. If <code>alpha</code> is set then <code>mu</code> and <code>bounds</code> are ignored with a warning.</dd>

</dl>

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

fastBM: (Reasonably) fast quantitative trait simulation on phylogenies

Description

Usage

Value

Arguments

Author

References

See Also

Examples