mgroup: Mantel test for groups

Description

Simple and partial Mantel tests, with options for ranked data, permutation tests, and bootstrapped confidence limits.

Usage

mgroup(edist, groups, nperm=1000)

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.

Value

nclust

Number of groups tested.

mantelr

Mantel coefficient.

pval1

one-tailed p-value (null hypothesis: r <= 0).

Details

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

References

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

Examples

Run this code

# NOT RUN {
# 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)

# }

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