force.ultrametric

an object of class <code>"phylo"</code>.

tree

the method to use to force the tree to be ultrametric. Options are <code>"nnls"</code> (which uses the phangorn function <code><a rd-options="" href="/link/nnls.tree?package=phytools&version=0.7-20" data-mini-rdoc="phytools::nnls.tree">nnls.tree</a></code> internally), or <code>"extend"</code>.

method

This function forces an object of class <code>"phylo"</code> to be ultrametric. This is achieved either by using <code><a rd-options="" href="/link/nnls.tree?package=phytools&version=0.7-20" data-mini-rdoc="phytools::nnls.tree">nnls.tree</a></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><a rd-options="" href="/link/is.ultrametric?package=phytools&version=0.7-20" data-mini-rdoc="phytools::is.ultrametric">is.ultrametric</a></code> for reasons of numerical precision.

utilities

Statistics

A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which 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, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or 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

the method to use to force the tree to be ultrametric. Options are <code>"nnls"</code> (which uses the phangorn function <code><a rd-options='' href='nnls.tree'>nnls.tree</a></code> internally), or <code>"extend"</code>.

This function forces an object of class <code>"phylo"</code> to be ultrametric. This is achieved either by using <code><a rd-options='' href='nnls.tree'>nnls.tree</a></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><a rd-options='' href='is.ultrametric'>is.ultrametric</a></code> for reasons of numerical precision.

force.ultrametric: Forces a phylogenetic tree to be ultrametric

Description

Usage

Arguments

Value

References

See Also