reduce_tree

Function to remove speciation events occuring after an extinction event.
Extinct species are pruned randomly, such that only a single extinct species
per branching event (if any extinct species) remains.

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

reduce_tree function

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

Arguments

Function to remove speciation events occuring after an extinction event.
Extinct species are pruned randomly, such that only a single extinct species
per branching event (if any extinct species) remains. — reduce_tree

<dl>

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

</dl>

Function to remove speciation events occuring after an extinction event.
Extinct species are pruned randomly, such that only a single extinct species
per branching event (if any extinct species) remains.

reduce_tree: Function to remove speciation events occuring after an extinction event. Extinct species are pruned randomly, such that only a single extinct species per branching event (if any extinct species) remains.

Description

Usage

Value

Arguments