integration.Vrel: Quantify integration in a set of traits

In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data

Quantify integration in a set of traits

Description

Function quantifies the morphological integration in a set of traits

Usage

integration.Vrel(A, phy = NULL)

Arguments

A	A 3D array (p x k x n) containing Procrustes shape variables for all specimens, or a matrix (n x variables)
phy	A phylogenetic tree of class phylo - see read.tree in library ape

Details

The function quantifies the strength of morphological integration in a set of variables. Here the set of traits are treated as a single unit, and the overall degree of covariation in them is quantified using the relative eigenvalue index: Vrel (Pavlicev et al. 2009). Following Conaway and Adams (2022), only the non-trivial dimensions of variation are used in the calculation of Vrel. The measure is then converted to an effect size (Z-score), based on the procedures in Conaway and Adams (2022). These may be used in subsequent comparisons of the strength of integration across datasets. Input for the analysis may be a 3D array of Procrustes coordinates, of a matrix of variables. If the observations are species related by a phylogeny, the phylogeny may also be included.

Value

Objects of class "rel.eig" from integration.Vrel return a list of the following:

Re.obs	The observed relative eigenvalue index (Vrel).
Z.obs	The associated Z-score, which represents the effect size of Vrel.
ZR	The effect size translated to a positive scale (so that no integration is ZR = 0).
ZR.var	The variance of the effect size.

Author(s)

Dean Adams

References

Pavlicev, M., J. M. Cheverud, and G. P. Wagner. 2009. Measuring morphological integration using eigenvalue variance. Evolutionary Biology 36:157-170.

Conaway, M.A., and D.C. Adams. 2022. An effect size for comparing the strength of morphological integration across studies. Evolution. (Accepted).

See Also

compare.ZVrel

Examples

data(plethodon) 
Y.gpa<-gpagen(plethodon$land)    #GPA-alignment    
integration.Vrel(Y.gpa$coords)

EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.