skewers {phytools}

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.