calc_required_node_time

calculates the required node time to obtain a desired fraction
of substitutions at the node

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

calc_required_node_time function

<dl><dt>phy</dt>
<dd>phylogenetic tree</dd>
<dt>s</dt>
<dd>desired fraction</dd>
<dt>model</dt>
<dd>node substitution model, either "linked" or "unlinked".</dd></dl>

Arguments

Calculate the required node time to obtain a desired fraction of
substitutions at the node — calc_required_node_time

<dl>

<dt>phy</dt>
<dd>phylogenetic tree</dd>


<dt>s</dt>
<dd>desired fraction</dd>


<dt>model</dt>
<dd>node substitution model, either "linked" or "unlinked".</dd>

</dl>

calc_required_node_time: Calculate the required node time to obtain a desired fraction of substitutions at the node

Description

Usage

Value

Arguments