Dtest

set of stochastic map trees (i.e., object of class <code>"multiSimmap"</code> for character 1. Note that <code>t1</code> and <code>t2</code> should be of the same length.

set of stochastic map trees (i.e., object of class <code>"multiSimmap"</code> for character 2. Note that <code>t1</code> and <code>t2</code> should be of the same length.

number of simulations to use in the test.

nsim

arguments to be passed internally to <code>make.simmap</code>. Note that (for now) these must be the same for both <code>t1</code> and <code>t2</code> (that is to say, we are not able to assume different trait evolution models for each tree).

This function conducts the 'D-test' of Huelsenbeck et al. (2003).

Simulation

phylogenetics

comparative method

Bayesian

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.

Dtest: Conducts correlational D-test from stochastic mapping

Description

Usage

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Value

Details

References

See Also