skewers: Matrix comparison using the method of random skewers

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Matrix comparison using the method of random skewers

Description

Performs the random skewers matrix comparison method of Cheverud (1996).

Usage

skewers(X, Y, nsim=100, method=NULL)

Arguments

X	covariance matrix.
Y	covariance matrix.
nsim	number of random vectors.
method	method to generate a null distribution of the random skewers correlation between matrices. If method=NULL then the correlation will be compared to the correlation between random vectors; however this test has type I error substantially above the nominal level for ostensibly random matrices. Other values of method will be passed as covMethod to genPositiveDefMat for a more robust hypothesis test (see below). Recommended values include "unifcorrmat".

Details

This function performs the random skewers matrix comparison method of Cheverud (1996; also see Cheverud & Marroig 2007 for more details). In addition, it includes a more robust hypothesis test in which random covariance matrices are simulated under a variety of models, and then the mean correlation between response vectors to random skewers are computed.

Value

A list with the following components:

r	mean random skewers correlation.
p	p-value from simulation.

Author(s)

Liam Revell [e-mail]

References

Cheverud, J. M. (1996) Quantitative genetic analysis of cranial morphology in the cotton-top (Saguinus oedipus) and saddle-back (S. fuscicollis) tamarins. J. Evol. Biol., 9, 5–42.

Cheverud, J. M. and G. Marroig (2007) Comparing covariance matrices: Random skewers method compared to the common principal components model. Genetics & Molecular Biology, 30, 461–469.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

phytools documentation built on June 22, 2024, 10:39 a.m.