slow_matrix

this function calculates the p matrix within R
this is slower than the C++ implementation in <code>get_p_matrix</code>
but provides a way to debug and verify

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

slow_matrix function

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

Arguments

this function calculates the p matrix within R
this is slower than the C++ implementation in get_p_matrix
but provides a way to debug and verify — slow_matrix

<dl>

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


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


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

</dl>

this function calculates the p matrix within R
this is slower than the C++ implementation in <code>get_p_matrix</code>
but provides a way to debug and verify

slow_matrix: this function calculates the p matrix within R this is slower than the C++ implementation in `get_p_matrix` but provides a way to debug and verify

Description

Usage

Value

Arguments