GraphGeodesic

Cophenetic

Graph Geodesic between leaves of unweighted tree

internal

Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.

Martin R. Smith

Rogue

Identify Rogue Taxa in Sets of Phylogenetic Trees

Andre J. Aberer

GraphGeodesic function

<dl><dt>x</dt>
<dd>Object of class <code>phylo</code>.</dd>
<dt>nTip</dt>
<dd>Integer specifying number of leaves.</dd>
<dt>asMatrix</dt>
<dd>Logical specifying whether to coerce output to matrix format.</dd></dl>

Arguments

Martin R. Smith, modifying algorithm by Emmanuel Paradis
in <code>ape::dist.nodes()</code>.

Author

Graph Geodesic between leaves of unweighted tree — GraphGeodesic

<dl>

<dt>x</dt>
<dd>Object of class <code>phylo</code>.</dd>


<dt>nTip</dt>
<dd>Integer specifying number of leaves.</dd>


<dt>asMatrix</dt>
<dd>Logical specifying whether to coerce output to matrix format.</dd>

</dl>

GraphGeodesic: Graph Geodesic between leaves of unweighted tree

Description

Usage

Value

Arguments

Author

Examples