Doesn't replicate reflect this fine spatial arrangement sufficiently?

On Dec 26, 2010 9:52 PM, <Anna.Richards@csiro.au> wrote:
> 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@ub.edu]
> Sent: Saturday, December 25, 2010 6:53 AM
> To: Andrew Dolman
> Cc: Richards, Anna (CES, Darwin); r-sig-mixed-models@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.
>
>
> --
> ---------------------------------------
> José M. Blanco Moreno
>
> Dept. de Biologia Vegetal (Botànica)
> Universitat de Barcelona
> Av. Diagonal 645
> 08028 Barcelona SPAIN
> ---------------------------------------
>
> phone: (+34) 934 039 863
> fax: (+34) 934 112 842
> e-mail: jmblanco@ub.edu
>
>

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