geomorph (version 2.0.1)

pairwiseD.test: Pairwise Group Comparisons

Description

Function performs pairwise comparisons among groups using the Euclidean distances among group means.

Usage

pairwiseD.test(y, x, iter = 999)

Arguments

y

A two-dimensional array of shape data

x

A factor defining groups

iter

Number of iterations for permutation test

Value

• Function returns a list with the following components:
• Dist.obs
  A matrix of Euclidean distances among group means
• Prob.Dist
  A matrix of pairwise significance levels based on permutation

Details

The function performs pairwise comparisons to identify shape among groups. The function is designed as a post-hoc test to Procrustes ANOVA, where the latter has identified significant shape variation explained by a grouping factor. The function takes as input the shape data (y), and a grouping factor (x). It then estimates the Euclidean distances among group means, which are used as test values. These are then statistically evaluated through permutation, where the rows of the shape matrix are randomized relative to the grouping variable. The input for the shape data (y) must be in the form of a two-dimensional data matrix of dimension (n x [p x k]), rather than a 3D array. It is assumed that the landmarks have previously been aligned using Generalized Procrustes Analysis (GPA) [e.g., with gpagen]. The function two.d.array can be used to obtain a two-dimensional data matrix from a 3D array of landmark coordinates.

Examples

data(plethodon)
Y.gpa<-gpagen(plethodon$land)    #GPA-alignment
y<-two.d.array(Y.gpa$coords)
### Procrustes ANOVA
procD.lm(y~plethodon$species,iter=99)

### Pairwise comparisons
pairwiseD.test(y,plethodon$species,iter=99)