get_p_matrix

Simulate DNA sequences for the node substitution model.
In the node substitution model, substitutions accumulate additionally
during a speciation event, providing a potential mechanistic explanation for
substitution rate variation. This package provides tools to simulate
such a process, simulate a reference process with only substitutions along
the branches, and provides tools to infer phylogenies from alignments. More
information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.

Thijs Janzen

nodeSub

Simulate DNA Alignments Using Node Substitutions

get_p_matrix function

<dl><dt>branch_length</dt>
<dd>branch length</dd>
<dt>eig</dt>
<dd>eigen object</dd>
<dt>rate</dt>
<dd>rate</dd></dl>

Arguments

calculate p matrix — get_p_matrix

<dl>

<dt>branch_length</dt>
<dd>branch length</dd>


<dt>eig</dt>
<dd>eigen object</dd>


<dt>rate</dt>
<dd>rate</dd>

</dl>

get_p_matrix: calculate p matrix

Description

Usage

Value

Arguments