minRotate

tipRotate

tree

<p>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 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>.</p>

<p>This function 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>.</p>

utilities

phylogenetics

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.

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

Description

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