[R-sig-eco] WG: Re: clustering with random effect

[Jana Buerger]

David,

to be honest I have used the terminology of sites and species only
analogously to make it easier to explain what a method I'm looking for.

In fact, I'm analysing pesticide use data. my sites are different
fields, the species are different pesticide treatments, for example a
number of fungicide treatments. Data in the matrix are numbers between
approx. 0 and 2.5 and stand for the amount of the treatment. There are
many fields from altogether 7 farms.
Now, i used clustering and PCA for analysing patterns of treatment,
and afterwards RDA to find important crop management factors influencing
patterns.

As I described inthe original post, in an RDA with a conditioning term
on "Farm" (or study area) the clusters don't separate anymore as in
unconditioned RDA.

Now, I wonder if I can have a clustering of sites with a conditioning
term on "Farm" sort of removed before clustering.

thanks for your help.

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

----- Originalnachricht -----
Von: Farrar.David at epamail.epa.gov
Datum: Donnerstag, April 2, 2009 8:25 pm
Betreff: Re: [R-sig-eco] clustering with random effect
An: Jana Buerger <jana.buerger at uni-rostock.de>

> Jana,
> 
> I do not necessarily have an answer for you, but your problem 
> sounds 
> interesting. 
> 
> Dan you explain more clearly how your data collection is designed?  
> Also, 
> what are your 
> clusters supposed to represent in ecological terms?  Clusters of 
> sites or 
> clusters of 
> species?
> 
> David 
> 
> 
> 
> From:
> Jana Buerger <jana.buerger at uni-rostock.de>
> To:
> r-sig-ecology at r-project.org
> Date:
> 04/02/2009 07:49 AM
> Subject:
> [R-sig-eco] clustering with random effect
> 
> 
> 
> 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 
> controllingfor 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 
> thecondition (CCA$Xbar)? or is this mixing up distance based with 
> vectorbased 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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