mgroup: Mantel test for groups

In phiala/ecodist: Dissimilarity-Based Functions for Ecological Analysis

Mantel test for groups

Description

Mantel test across one or more group contrasts.

Usage

mgroup(edist, groups, nperm = 1000, mrank = FALSE)

Arguments

edist	a dist object or lower triangular distance vector.
groups	a vector of group memberships (numeric, character, or factor), or a matrix or data frame with columns describing multiple sets of groups.
nperm	number of permutations to use. If set to 0, the permutation test will be omitted.
mrank	if this is set to FALSE (the default option), Pearson correlations will be used. If set to TRUE, the Spearman correlation (correlation ranked distances) will be used.

Details

mgroup returns the Mantel correlations for group contrast matrices computed from cluster groups across a range of clustering levels.

Value

nclust	Number of groups tested.
mantelr	Mantel coefficient.
pval1	one-tailed p-value (null hypothesis: r <= 0).

Author(s)

Sarah Goslee

References

Legendre, P. and M. Fortin. 1989. Spatial pattern and ecological analysis. Vegetatio 80:107-138.

See Also

mantel

Examples

# Using a model matrix to test group membership

data(iris)
iris.d <- dist(iris[,1:4])
mgroup(iris.d, iris[,5])

# clustering-based example

data(graze)
graze.d <- dist(graze[, -c(1:2)])
graze.hclust <- hclust(graze.d)

clust.groups <- data.frame(
	k2 = cutree(graze.hclust, k = 2),
	k4 = cutree(graze.hclust, k = 4),
	k6 = cutree(graze.hclust, k = 6),
	k8 = cutree(graze.hclust, k = 8))

mgroup(graze.d, clust.groups, nperm=1000)

phiala/ecodist documentation built on Nov. 5, 2023, 10:47 a.m.