DoubleNNI

Returns the edge parameter of the two trees consistent with the speficied <acronym>NNI</acronym> rearrangement

internal

Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.

Martin R. Smith

TreeSearch

Phylogenetic Analysis with Discrete Character Data

Martin Brazeau

DoubleNNI function

<dl><dt>parent</dt>
<dd>Integer vector corresponding to the first column of the edge
matrix of a tree of class <code>phylo</code>, i.e.
<code>tree[["edge"]][, 1]</code></dd>
<dt>child</dt>
<dd>Integer vector corresponding to the second column of the edge
matrix of a tree of class <code>phylo</code>, i.e.
<code>tree[["edge"]][, 2]</code>.</dd>
<dt>edgeToBreak</dt>
<dd>In (<code>Rooted</code>/<code>Double</code>)<code>NNI()</code>, an optional integer
specifying the index of an edge to rearrange, generated randomly if not
specified.
If <code>-1</code>, a complete list of all trees one step from the input tree
will be returned.
In <code>cNNI()</code>, an integer from zero to <code>nEdge(tree) - nTip(tree) - 2</code>,
specifying which internal edge to break.</dd></dl>

Arguments

Author

Double NNI — DoubleNNI

<dl>

<dt>parent</dt>
<dd>Integer vector corresponding to the first column of the edge
matrix of a tree of class <code>phylo</code>, i.e.
<code>tree[["edge"]][, 1]</code></dd>


<dt>child</dt>
<dd>Integer vector corresponding to the second column of the edge
matrix of a tree of class <code>phylo</code>, i.e.
<code>tree[["edge"]][, 2]</code>.</dd>


<dt>edgeToBreak</dt>
<dd>In (<code>Rooted</code>/<code>Double</code>)<code>NNI()</code>, an optional integer
specifying the index of an edge to rearrange, generated randomly if not
specified.
If <code>-1</code>, a complete list of all trees one step from the input tree
will be returned.
In <code>cNNI()</code>, an integer from zero to <code>nEdge(tree) - nTip(tree) - 2</code>,
specifying which internal edge to break.</dd>

</dl>

DoubleNNI: Double NNI

Description

Usage

Value

Arguments

Author