Consistency

<code>Consistency()</code> calculates the so-called consistency and retention 'indices'
for each character in a dataset, given a bifurcating tree.
Although there is not a straightforward interpretation of these indices,
they are sometimes taken as an indicator of the fit of a character to a
tree. Values correlate with the number of species sampled and the
distribution of taxa between character states, so are not strictly comparable
between characters in which these factors differ.

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 Morphological Data

Martin Brazeau

Consistency function

<dl><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>tree</dt>
<dd>A tree of class <code>phylo</code>.</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

<a href="https://smithlabdurham.github.io/">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeSearch&version=1.1.2" data-mini-rdoc="TreeSearch::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Consistency / retention 'indices' — Consistency

<dl>

<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>tree</dt>
<dd>A tree of class <code>phylo</code>.</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>

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

Consistency: Consistency / retention 'indices'

Description

Usage

Value

Arguments

Author

Details

Examples