force.ultrametric

This function coerces an object of class <code>"phylo"</code> to be ultrametric.	
This is achieved either by using <code>nnls.tree</code> from the phangorn package to compute the set of edge lengths that result in a minimized sum-of-squares distance between the patristic distance of the output and input trees (<code>method="nnls"</code>); or by simply extending all the external edges of the tree to match the external edge with the greatest total height (<code>method="extend"</code>).	
Note that neither of these should be treated as formal statistical methods for inferring an ultrametric tree. Rather, this method can be deployed when a genuinely ultrametric tree read from file fails <code>is.ultrametric</code> for reasons of numerical precision.

utilities

Statistics

A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

force.ultrametric function

<dl>	<dt>tree</dt>
<dd>an object of class <code>"phylo"</code>.</dd>	<dt>method</dt>
<dd>the method to use to force the tree to be ultrametric. Options are <code>"nnls"</code> (which uses the phangorn function <code>nnls.tree</code> internally), or <code>"extend"</code>.</dd>	<dt>...</dt>
<dd>optional arguments: principally, <code>message</code>. This argument (if set to <code>FALSE</code>) can be used to suppress the default warning message that <code>force.ultrametric</code> should not be used as a formal statistical method to ultrametricize a tree.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.2-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Forces a phylogenetic tree to be ultrametric — force.ultrametric

<dl>

	<dt>tree</dt>
<dd>an object of class <code>"phylo"</code>.</dd>

	<dt>method</dt>
<dd>the method to use to force the tree to be ultrametric. Options are <code>"nnls"</code> (which uses the phangorn function <code>nnls.tree</code> internally), or <code>"extend"</code>.</dd>

	<dt>...</dt>
<dd>optional arguments: principally, <code>message</code>. This argument (if set to <code>FALSE</code>) can be used to suppress the default warning message that <code>force.ultrametric</code> should not be used as a formal statistical method to ultrametricize a tree.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

force.ultrametric: Forces a phylogenetic tree to be ultrametric

Description

Usage

Value

Arguments

Author

References

See Also