You would be better off posting to R-sig-mixed-models or R-sig-ecology
-- Bert
On Thu, Nov 18, 2010 at 9:58 AM, Simon Garnier <sgarnier at princeton.edu>
wrote:> Dear all,
>
> I'm discovering the somehow confusing (for me) world of linear mixed
models after having been advised it could be the best option to analyze my
dataset. After several days of reading, I'm not sure that what I ended up
with makes some sense and I'd greatly appreciate any help and explanations.
>
> The dataset has been obtained as follows. In 15 different locations, I
counted during 10 seconds the number of ants crossing a gap, before and after
destroying a bridge that ants had previously built over the gap. I then waited
for the ants to rebuild the bridge and repeated two more times the counting and
destroying process. Therefore, for each gap observed, I have 3 replicates of the
same experiment, each of them providing 1 count value for each treatment tested
(before and after bridge destruction), i.e. 6 values in total per gap. I also
measured for each gap its length.
>
> I now want to model the effect of the gap length (GapLength, continuous
variable), the treatment (Treatment, categorical variable) and the replicate
position (Replicate, categorical variable) on the number of ants crossing the
gap (AntCount, count variable). As far as I understand, the gap (Gap) can be
treated here as a random effect, the gap length, the treatment and the replicate
position as fixed effects. Moreover, the treatment variable is nested in the
replicate position variable that is also nested in the gap variable. Finally,
since I have count data, a poisson distribution should be used for the model.
With all this information in mind and some additional information from various
sources, I ended up with the following R code:
>
> lmer(AntCount ~ Treatment + GapLength + (Treatment | Gap / Replicate) +
(GapLength | Gap), data=dat, family=poisson(link=log))
>
> The code runs fine and does not return any error. But of course this does
not mean the model was correctly designed. Am I right when I'm doing this or
am I (most likely) completely wrong?
>
> Thanks in advance for your help.
>
> Best,
> Simon.
>
> --
>
--------------------------------------------------------------------------------
> Dr. Simon Garnier
> Department of Ecology & Evolutionary Biology
> Princeton University
> Guyot Hall
>
> e-mail: sgarnier at princeton.edu / simon.garnier at gmail.com
> website: http://www.simongarnier.com
> photoblog: http://www.simongarnier.org
>
--------------------------------------------------------------------------------
>
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--
Bert Gunter
Genentech Nonclinical Biostatistics