phytools: skewers – R documentation

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skewers

Matrix comparison using the method of random skewers

Description

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.

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"`.

Value

A list with the following components:

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

Author(s)

Liam Revell liam.revell@umb.edu

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

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19