Mantel test for groups
Simple and partial Mantel tests, with options for ranked data, permutation tests, and bootstrapped confidence limits.
mgroup(edist, groups, nperm=1000)
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. |
mgroup returns the Mantel correlations for group contrast
matrices computed from cluster groups across a range of clustering
levels.
nclust |
Number of groups tested. |
mantelr |
Mantel coefficient. |
pval1 |
one-tailed p-value (null hypothesis: r <= 0). |
Sarah Goslee
Legendre, P. and M. Fortin. 1989. Spatial pattern and ecological analysis. Vegetatio 80:107-138.
# 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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