generate_design_matrix

Constructs a design matrix for a given phylogenetic tree, used in Ornstein-Uhlenbeck modeling.

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

generate_design_matrix function

<dl><dt>tree</dt>
<dd>A phylogenetic tree of class <code>phylo</code>.</dd>
<dt>type</dt>
<dd>A character string specifying the type of design matrix to generate. Options are <code>"simpX"</code> or <code>"orgX"</code>.</dd>
<dt>alpha</dt>
<dd>The selection strength parameter (only used when <code>type = "orgX"</code>).</dd></dl>

Arguments

Generate Design Matrix — generate_design_matrix

<dl>

<dt>tree</dt>
<dd>A phylogenetic tree of class <code>phylo</code>.</dd>


<dt>type</dt>
<dd>A character string specifying the type of design matrix to generate. Options are <code>"simpX"</code> or <code>"orgX"</code>.</dd>


<dt>alpha</dt>
<dd>The selection strength parameter (only used when <code>type = "orgX"</code>).</dd>

</dl>

generate_design_matrix: Generate Design Matrix

Description

Usage

Value

Arguments