calc_expected_hidden_nodes

Calculate the number of expected hidden nodes
using equation 1 in Manceau et al. 2020

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_expected_hidden_nodes function

<dl><dt>phy</dt>
<dd>phylogenetic tree</dd>
<dt>lambda</dt>
<dd>birth rate</dd>
<dt>mu</dt>
<dd>death rate</dd></dl>

Arguments

Calculate the number of expected hidden nodes in a phylogenetic tree — calc_expected_hidden_nodes

<dl>

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


<dt>lambda</dt>
<dd>birth rate</dd>


<dt>mu</dt>
<dd>death rate</dd>

</dl>

calc_expected_hidden_nodes: Calculate the number of expected hidden nodes in a phylogenetic tree

Description

Usage

Value

Arguments

References