count_hidden

Function to calculate the number of hidden speciation events, e.g. speciation
events that have lead to an extinct species. Thus, these hidden speciation
events can only be detected in complete trees (as opposed to reconstructed
trees).

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

count_hidden function

<dl><dt>tree</dt>
<dd>phylo object</dd></dl>

Arguments

Function to calculate the number of hidden speciation events, e.g. speciation
events that have lead to an extinct species. Thus, these hidden speciation
events can only be detected in complete trees (as opposed to reconstructed
trees). — count_hidden

<dl>

<dt>tree</dt>
<dd>phylo object</dd>

</dl>

Function to calculate the number of hidden speciation events, e.g. speciation
events that have lead to an extinct species. Thus, these hidden speciation
events can only be detected in complete trees (as opposed to reconstructed
trees).

count_hidden: Function to calculate the number of hidden speciation events, e.g. speciation events that have lead to an extinct species. Thus, these hidden speciation events can only be detected in complete trees (as opposed to reconstructed trees).

Description

Usage

Value

Arguments