NexusTokensToInteger

<code>NexusTokensToInteger()</code> converts the character matrix returned by
<code>ReadCharacters()</code> to an integer matrix, mapping polymorphic,
ambiguous (<code>?</code>), and inapplicable (<code>-</code>) tokens to <code>NA_integer_</code> or to the
first/last state listed in the polymorphism, depending on <code>polymorphism</code>.

Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.

Martin R. Smith

TreeTools

Create, Modify and Analyse Phylogenetic Trees

Emmanuel Paradis

Robert Noble

NexusTokensToInteger function

<dl><dt>tokens</dt>
<dd>Character matrix as returned by <code>ReadCharacters()</code>, a
character vector as returned by <code>NexusTokens()</code>, or a <code>phyDat</code> object.</dd>
<dt>polymorphism</dt>
<dd>Character string specifying how to handle polymorphic
tokens such as <code>"(01)"</code> or <code>"{12}"</code>:<dl>
<dt><code>"?"</code> (default)</dt>
<dd>Treat as the NEXUS missing-data token: map to
<code>NA_integer_</code>.</dd></dl></dd><dt><code>"first"</code></dt>
<dd>Use the first state digit inside the brackets.</dd><dt><code>"last"</code></dt>
<dd>Use the last state digit inside the brackets.</dd>
</dl>Tokens <code>"?"</code> and <code>"-"</code> always map to <code>NA_integer_</code> regardless of
<code>polymorphism</code>.

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeTools&version=2.4.1" data-mini-rdoc="TreeTools::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Convert Nexus token matrix to integer — NexusTokensToInteger

<dl>

<dt>tokens</dt>
<dd>Character matrix as returned by <code>ReadCharacters()</code>, a
character vector as returned by <code>NexusTokens()</code>, or a <code>phyDat</code> object.</dd>


<dt>polymorphism</dt>
<dd>Character string specifying how to handle polymorphic
tokens such as <code>"(01)"</code> or <code>"{12}"</code>:<dl>
<dt><code>"?"</code> (default)</dt>
<dd>Treat as the NEXUS missing-data token: map to
<code>NA_integer_</code>.</dd>

<dt><code>"first"</code></dt>
<dd>Use the first state digit inside the brackets.</dd>

<dt><code>"last"</code></dt>
<dd>Use the last state digit inside the brackets.</dd>


</dl>Tokens <code>"?"</code> and <code>"-"</code> always map to <code>NA_integer_</code> regardless of
<code>polymorphism</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>)

NexusTokensToInteger: Convert Nexus token matrix to integer

Description

Usage

Value

Arguments

Author

Details

See Also

Examples