[R-sig-eco] mixed effect model: compare seed families

[ONKELINX, Thierry]

Dear Zoltan,

You random effects are not nested but crossed. Use lmer from the lme4
package for that kind of problem.

lmer(Y ~ soil * mother_size + (1|plot) + (1|site/seed_family)) 

HTH,

Thierry


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium

tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] Namens Zoltan Botta-Dukat
Verzonden: maandag 18 januari 2010 20:27
Aan: r-sig-ecology at r-project.org
Onderwerp: [R-sig-eco] mixed effect model: compare seed families

Hi everyone,

I'm struggling with evaluation an experiment for maternal effect and
plasticity.

We have grown offsprings of 64 individuals (seed families) in a common
garden experiment. There was 8 replicate plots, in each plot one
individual from each seed family.
Seeds come from 8 different sites, and 8 seed families collected in each
site. Sites belong to two groups according to soil type: sand and clay. 
In each site 4 large and 4 small mother plant were chosen.

We would like to test:
- difference between soil types
- difference between mother size categories
- interaction between soil type and mother size
- difference between sites within a soil type (In fact we are interested
in differences between sites in sand only, because the common garden was
on sand, and one site is situated in its neighbour).

It is clear that soil_type and mother_size are fix factors.
I suspect that both plot and seed_family should be random factor, but
I'm not sure what is the correct specification. Maybe
random=~1|plot/seed_family. It's OK?
Can I include the comparison between sites into this model? Or would be
better to make a separate analysis using seed families from sand only?

Thanks for the suggestions

Zoltan

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Druk dit bericht a.u.b. niet onnodig af.
Please do not print this message unnecessarily.

Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message 
and any annex are purely those of the writer and may not be regarded as stating 
an official position of INBO, as long as the message is not confirmed by a duly 
signed document.