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

[Dunbar, Michael]

Hi Zoltan

Possibly plot and source site are crossed. ie (1|plot) + (1|site) in lmer (not nlme)

There would then be no problem in having fixed effects corresponding to sites and properties of individuals. As site is random, you can test sand vs clay, but a test of residual differences between sites is tested by comparing models with and without the site random effect. If you just want to test this within sand then just fit the models to the sand site data, but you then many be running short of replication?

You don't mention your response variable, is each individual measured more than once, of not then you can't specify an individual as random as there is no replication within it.

regards

Mike


________________________________________
From: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] On Behalf Of Zoltan Botta-Dukat [bdz at botanika.hu]
Sent: 18 January 2010 19:26
To: r-sig-ecology at r-project.org
Subject: [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

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