.StatusToMatrix

.StatusToArray

Converts a vector to a matrix that can be analysed by the <code>DoNotConflict()</code>
function family.

internal

Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress
(1986), Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of binary trees.

Martin R. Smith

Quartet

Comparison of Phylogenetic Trees Using Quartet and Split
Measures

Andreas Sand

Gerth Stølting Brodal

Rolf Fagerberg

Thomas Mailund

Christian N. S. Pedersen

Jens Johansen

Morten K. Holt

.StatusToMatrix function

<dl><dt>statusVector</dt>
<dd>Either (i) a named vector of integers, with
names <code>N</code>, <code>s</code>, <code>r1</code>, <code>r2</code>, either <code>d</code> or <code>d1</code> and <code>d2</code>, and optionally <code>u</code>;
or (ii) a matrix whose named rows correspond to the same quantities.</dd>
<dt>status</dt>
<dd>A named three-dimensional array of integers, with slices
named <code>s</code>, <code>r1</code>, <code>r2</code>, either <code>d</code> or <code>d1</code> and <code>d2</code>, and either <code>N</code> or <code>u</code>.</dd></dl>

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=Quartet&version=1.2.6" data-mini-rdoc="Quartet::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Status vector to matrix — .StatusToMatrix

<dl>

<dt>statusVector</dt>
<dd>Either (i) a named vector of integers, with
names <code>N</code>, <code>s</code>, <code>r1</code>, <code>r2</code>, either <code>d</code> or <code>d1</code> and <code>d2</code>, and optionally <code>u</code>;
or (ii) a matrix whose named rows correspond to the same quantities.</dd>


<dt>status</dt>
<dd>A named three-dimensional array of integers, with slices
named <code>s</code>, <code>r1</code>, <code>r2</code>, either <code>d</code> or <code>d1</code> and <code>d2</code>, and either <code>N</code> or <code>u</code>.</dd>

</dl>

<a href='https://orcid.org/0000-0001-5660-1727'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

.StatusToMatrix: Status vector to matrix

Description

Usage

Value

Arguments

Author

Examples