evolvcv.lite

an object of class <code>"simmap"</code>. If <code>tree</code> is an object of class <code>"phylo"</code> then a simple multivariate Brownian motion model will be fit to the data in <code>X</code>.

tree

an <code>n</code> x <code>m</code> matrix of tip values for <code>m</code> continuously valued traits in <code>n</code> species - row names should be species names.

an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees.

maxit

tolerance value for <code>"L-BFGS-B"</code> optimization.

This function takes an object of class <code>"simmap"</code> with a mapped binary or multistate trait and data for two and only two continuously valued character. It then fits four different evolutionary models: common rates and correlation; different rates, common correlation; different correlations, common rates; no common structure.

phylogenetics

maximum likelihood

comparative method

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.

evolvcv.lite: Likelihood test for a shift in the evolutionary correlation between traits

Description

Usage

Arguments

Value

References

See Also