[R-sig-ME] design of nested mixed effects model with repeated measures

[Anna.Richards at csiro.au]

Thanks Jose and Andrew for the advice, especially so close to Christmas!

I included patch (or canopy type) in the random part of the model because I thought that the three samples taken from each patch type within a fire treatment are more closely related spatially than samples from other fire treatment. (Each 'patch' sample 'pseudo-replicate' was taken from beneath or far from a different tree canopy across the 1 hectare fire treatment plots). Does this mean I should nest patch within block in the random effects?

ie. y~patch*date*block, random=~1|block/patch/replicate  

Thanks again,
Anna
________________________________________
From: José Manuel Blanco Moreno [jmblanco at ub.edu]
Sent: Saturday, December 25, 2010 6:53 AM
To: Andrew Dolman
Cc: Richards, Anna (CES, Darwin); r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] design of nested mixed effects model with repeated measures

El 24/12/2010 17:45, Andrew Dolman escribió:
> Patch is not random either and even if it were it only has 2 levels
> and so cannot properly be fit as random. It's also crossed with block
> and with fire. (It's also a confusing name. Consider calling it
> habitat, or canopy(T,F))
>
I may be misunderstanding the design, but I would be somewhat reluctant to throw
away the random effect for patch. Indeed I think that Andrew is right when
considering renaming this factor as canopy or habitat (a factor wih two levels);
however, if the "replicates" are taken from beneath a single canopy (instead of
selecting different canopies from a plot), should not this nesting be included
in the random effects, even if the structure seems complicated?
Moreover, I do not think that canopy and plot are crossed, since you cannot move
one canopy from one plot to another, and each canopy on each plot is actually a
different individual.
Forgive me if I got it completely wrong. And merry Christmas by the way.


--
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José M. Blanco Moreno

Dept. de Biologia Vegetal (Botànica)
Universitat de Barcelona
Av. Diagonal 645
08028 Barcelona SPAIN
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phone: (+34) 934 039 863
fax: (+34) 934 112 842
e-mail: jmblanco at ub.edu