.CombineResults

.ReplaceResults

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

.CombineResults function

<dl><dt>x, y</dt>
<dd>3D arrays, each slice containing an edge matrix from a tree
of class <code>phylo</code>. <code>x</code> should not contain duplicates.</dd>
<dt>stage</dt>
<dd>Integer specifying element of <code>firstHit</code> in which new hits
should be recorded.</dd>
<dt>old</dt>
<dd>old array of edge matrices with <code>firstHit</code> attribute.</dd>
<dt>new</dt>
<dd>new array of edge matrices.</dd></dl>

Arguments

<a href="https://smithlabdurham.github.io/">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeSearch&version=1.5.1" data-mini-rdoc="TreeSearch::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Combine two edge matrices — .CombineResults

<dl>

<dt>x, y</dt>
<dd>3D arrays, each slice containing an edge matrix from a tree
of class <code>phylo</code>. <code>x</code> should not contain duplicates.</dd>


<dt>stage</dt>
<dd>Integer specifying element of <code>firstHit</code> in which new hits
should be recorded.</dd>


<dt>old</dt>
<dd>old array of edge matrices with <code>firstHit</code> attribute.</dd>


<dt>new</dt>
<dd>new array of edge matrices.</dd>

</dl>

<a href='https://smithlabdurham.github.io/'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

.CombineResults: Combine two edge matrices

Description

Usage

Value

Arguments

Author