TipTimedTree

<code>TipTimedTree()</code> plots a phylogenetic tree against time using an
ad hoc approach based on dates associated with the leaves.
Nodes are dated to the youngest possible value, plus an additional "buffer"
(specified with <code>minEdge</code>) to ensure that branching order is readable.

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

TipTimedTree function

<dl><dt>tree</dt>
<dd>A tree of class <code>phylo</code>.</dd>
<dt>tipAge</dt>
<dd>Numeric vector specifying the age (in units-of-time ago)
associated with each tip in <code>tree$tip.label</code> in turn.
Older ages signify earlier tips.</dd>
<dt>minEdge</dt>
<dd>Minimum length of edge to allow (in units-of-time)</dd></dl>

Arguments

Display time-calibrated tree using tip information only — TipTimedTree

<dl>

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


<dt>tipAge</dt>
<dd>Numeric vector specifying the age (in units-of-time ago)
associated with each tip in <code>tree$tip.label</code> in turn.
Older ages signify earlier tips.</dd>


<dt>minEdge</dt>
<dd>Minimum length of edge to allow (in units-of-time)</dd>

</dl>

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TipTimedTree: Display time-calibrated tree using tip information only

Description

Usage

Value

Arguments

Details

See Also

Examples