[R-sig-eco] clustering with random effect

[Marcelino de la Cruz]

Maybe you are asking for some form of constrained clustering.

Try the palaeo package of Steve Juggins:

http://www.staff.ncl.ac.uk/staff/stephen.juggins/analysis.htm

HTH

Marcelino

At 11:53 02/04/2009, Jana Buerger wrote:
>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
>
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>R-sig-ecology mailing list
>R-sig-ecology at r-project.org
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________________________________

Marcelino de la Cruz Rot

Departamento de  Biología Vegetal
E.U.T.I. Agrícola
Universidad Politécnica de Madrid
28040-Madrid
Tel.: 91 336 54 35
Fax: 91 336 56 56
marcelino.delacruz at upm.es