geomorph (version 2.1.6)

morphol.disparity: Morphological disparity for one or more groups of specimens

Description

Function estimates morphological disparity and performs pairwise comparisons among groups.

Usage

morphol.disparity(A, groups, iter = 999)

Arguments

A

A matrix (n x [p x k]) or 3D array (p x k x n) containing GPA-aligned coordinates for a set of specimens

groups

A factor defining groups

iter

Number of iterations for permutation test

Value

• Function returns a list with the following components:
• Disp.obs
  A matrix of Procrustes variance for each group
• Prob.Dist
  A matrix of pairwise significance levels based on permutation

Details

The function estimates morphological disparity and performs pairwise comparisons to identify differences between groups. The function takes as input GPA-aligned shape data [e.g., gpagen] and a grouping factor, and estimates disparity as the Procrustes variance for each group, which is the sum of the diagonal elements of the group covariance matrix (e.g., Zelditch et al. 2012). The group Procrustes variances are used as test values, and these are then statistically evaluated through permutation, where the vectors of residuals are randomized among groups. The function can be used to obtain disparity for the whole dataset by using a dummy group factor assigning all specimens to one group, in which case only Procrustes variance is returned.

References

Zelditch, M. L., D. L. Swiderski, H. D. Sheets, and W. L. Fink. 2012. Geometric morphometrics for biologists: a primer. 2nd edition. Elsevier/Academic Press, Amsterdam.

Examples

data(plethodon)
Y.gpa<-gpagen(plethodon$land)    #GPA-alignment
morphol.disparity(Y.gpa$coords, groups=plethodon$site, iter = 99)