CharacterLength

FitchSteps

FastCharacterLength

Homoplasy length of each character in a dataset on a specified tree.

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

CharacterLength function

<dl><dt>tree</dt>
<dd>A tree of class <code>phylo</code>.</dd>
<dt>dataset</dt>
<dd>A phylogenetic data matrix of phangorn class
<code>phyDat</code>, whose names correspond to the labels of any accompanying tree.</dd>
<dt>compress</dt>
<dd>Logical specifying whether to retain the compression of a
<code>phyDat</code> object or to return a vector specifying to each individual
character, decompressed using the dataset's <code>index</code> attribute.</dd></dl>

Arguments

<ul>
<li><code>FastCharacterLength()</code>: Do not perform checks. Use with care: may cause
erroneous results or software crash if variables are in the incorrect format.</li>
</ul>

Functions

<a href="https://smithlabdurham.github.io/">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeSearch&version=1.5.0" data-mini-rdoc="TreeSearch::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author