[R-sig-eco] clustering with random effect

[Jana Buerger]

Hello all!

I am looking for an idea how a site-species-matrix could be clustered
after correcting for a random effect, p.ex. different study areas.

more detailed explanation:
i have clustered my site-species-matrix and visualised clusters in a
constrained ordination plot obtained through rda command in package
vegan. results between both methods seem to be consistent.
now, i introduced a condition into the rda, in order to correct for a
random effect of different farms from which the samples of the
site-species-matrix were obtained. the clusters visualized in the
conditioned and constrained ordination plot change, of course.

which way would be appropriate to cluster the matrix, after controlling
for the farm?

randomLCA seems to be able to handle categorial data only(presence
absence data in the site species matrix), although a random effect may
be included.

i wondered if I could use part of the rda/cca-object for a new
clustering: the transformed X-matrix after removing variance due to the
condition (CCA$Xbar)? or is this mixing up distance based with vector
based methods?

thank you.
i'd be grateful for any comments.


Jana Bürger
Universität Rostock
FG Phytomedizin
Satower Straße 48
18059 Rostock
Tel. 0381-498 3171