minRotate

tipRotate

Rotates all the nodes of the tree to try and minimize the different between the order of the tips and the rank-order of a numeric vector <code>x</code> or (in the case of <code>tipRotate</code>) the actual integer vector, <code>x</code>.

utilities

phylogenetics

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, 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 trait data. 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 phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range 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)

minRotate function

<dl>	<dt>tree</dt>
<dd>tree.</dd>	<dt>x</dt>
<dd>numeric vector.</dd>	<dt>...</dt>
<dd>optional arguments to be used by <code>tipRotate</code>. Presently optional arguments can be <code>fn</code>, function to be used to compute the distance between the order of the tip labels in <code>tree</code> and the numeric vector <code>x</code> (presently <code>fn=function(x) x^2</code> by default); <code>methods</code>, the method or methods of tree traversal (can be <code>"pre"</code>, <code>"post"</code>, or <code>c("pre","post")</code>, for pre-, post-, or both pre- and post-order tree traversal); <code>rotate.multi</code>, whether to rotate multifurcations in all possible ways using <code>rotate.multi</code> (defaults to <code>FALSE</code>); and <code>print</code>, a logical argument specifying whether to print the search progress or to behave quietly. Only the option <code>print</code> is available for <code>minRotate</code>.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=2.3-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Rotates all nodes of the tree to minimize the difference in order with a vector — minRotate

<dl>

	<dt>tree</dt>
<dd>tree.</dd>

	<dt>x</dt>
<dd>numeric vector.</dd>

	<dt>...</dt>
<dd>optional arguments to be used by <code>tipRotate</code>. Presently optional arguments can be <code>fn</code>, function to be used to compute the distance between the order of the tip labels in <code>tree</code> and the numeric vector <code>x</code> (presently <code>fn=function(x) x^2</code> by default); <code>methods</code>, the method or methods of tree traversal (can be <code>"pre"</code>, <code>"post"</code>, or <code>c("pre","post")</code>, for pre-, post-, or both pre- and post-order tree traversal); <code>rotate.multi</code>, whether to rotate multifurcations in all possible ways using <code>rotate.multi</code> (defaults to <code>FALSE</code>); and <code>print</code>, a logical argument specifying whether to print the search progress or to behave quietly. Only the option <code>print</code> is available for <code>minRotate</code>.</dd>

</dl>

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

minRotate: Rotates all nodes of the tree to minimize the difference in order with a vector

Description

Usage

Value

Arguments

Author

Details

References