R: Mantel test for groups

mgroup {ecodist} | R Documentation

## 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.

### 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)

[Package ecodist version 2.0.7 Index]