plot.ShiftModel

Plots a phylogenetic tree with trait values at the tips and highlights branches with detected shifts in optimal value (mean) and variance.

Implements statistical methods for detecting evolutionary shifts
in both the optimal trait value (mean) and evolutionary diffusion variance.
The method uses an L1-penalized optimization framework to identify branches
where shifts occur, and the shift magnitudes. It also supports the
inclusion of measurement error. For more details, see Zhang, Ho, and Kenney (2023) <doi:10.48550/arXiv.2312.17480>.

Wensha Zhang

ShiVa

Detection of Evolutionary Shifts in Both Optimal Value and
Variance

Lam Si Tung Ho

Toby Kenney

plot.ShiftModel function

<dl><dt>x</dt>
<dd>An object of class <code>ShiftModel</code>, typically returned by <code>fit_OU_mean_var()</code> or <code>ShiVa()</code>.</dd>
<dt>title</dt>
<dd>A character string specifying the plot title.</dd>
<dt>...</dt>
<dd>Additional arguments passed to <code>plot.phylo()</code>.</dd></dl>

Arguments

Plot Method for ShiftModel Objects — plot.ShiftModel

<dl>

<dt>x</dt>
<dd>An object of class <code>ShiftModel</code>, typically returned by <code>fit_OU_mean_var()</code> or <code>ShiVa()</code>.</dd>


<dt>title</dt>
<dd>A character string specifying the plot title.</dd>


<dt>...</dt>
<dd>Additional arguments passed to <code>plot.phylo()</code>.</dd>

</dl>

plot.ShiftModel: Plot Method for ShiftModel Objects

Description

Usage

Value

Arguments