plot.phylosimsignal

Plot signal estimation as a fraction of a Brownian Motion process.

A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.

Francois Keck

phylosignal

Exploring the Phylogenetic Signal in Continuous Traits

plot.phylosimsignal function

<dl><dt>x</dt>
<dd>an object of class <code>phylosimsignal</code>.</dd>
<dt>methods</dt>
<dd>a character vector giving the methods
(included in the <code>phylosimsignal</code> object) to plot.</dd>
<dt>traits</dt>
<dd>a character vector giving the traits
(included in the <code>phylosimsignal</code> object) to plot.</dd>
<dt>stacked.methods</dt>
<dd>If different methods have been used, should they
be plotted on the same graphic (<code>TRUE</code>) or not (<code>FALSE</code>, default).</dd>
<dt>stacked.traits</dt>
<dd>If different traits have been used, should they
be plotted on the same graphic (<code>TRUE</code>) or not (<code>FALSE</code>, default).</dd>
<dt>print.quantiles</dt>
<dd>logical stating whether quantiles should be plotted.</dd>
<dt>col</dt>
<dd>a vector of colors for the different methods.</dd>
<dt>legend</dt>
<dd>a logical. If <code>stacked.methods</code> is set to <code>TRUE</code>,
should a legend be printed to differentiate the different methods?</dd>
<dt>...</dt>
<dd>further arguments to be passed to or from other methods.</dd></dl>

Arguments

Plot signal estimation as a fraction of a Brownian Motion process. — plot.phylosimsignal

<dl>

<dt>x</dt>
<dd>an object of class <code>phylosimsignal</code>.</dd>


<dt>methods</dt>
<dd>a character vector giving the methods
(included in the <code>phylosimsignal</code> object) to plot.</dd>


<dt>traits</dt>
<dd>a character vector giving the traits
(included in the <code>phylosimsignal</code> object) to plot.</dd>


<dt>stacked.methods</dt>
<dd>If different methods have been used, should they
be plotted on the same graphic (<code>TRUE</code>) or not (<code>FALSE</code>, default).</dd>


<dt>stacked.traits</dt>
<dd>If different traits have been used, should they
be plotted on the same graphic (<code>TRUE</code>) or not (<code>FALSE</code>, default).</dd>


<dt>print.quantiles</dt>
<dd>logical stating whether quantiles should be plotted.</dd>


<dt>col</dt>
<dd>a vector of colors for the different methods.</dd>


<dt>legend</dt>
<dd>a logical. If <code>stacked.methods</code> is set to <code>TRUE</code>,
should a legend be printed to differentiate the different methods?</dd>


<dt>...</dt>
<dd>further arguments to be passed to or from other methods.</dd>

</dl>

plot.phylosimsignal: Plot signal estimation as a fraction of a Brownian Motion process.

Description

Usage

Arguments