[R-sig-eco] best choice of GLMM for seed set data

[Thierry Onkelinx]

Dear Mariano,

The binomial distribution (not error family) assumes that you have a
number of successes and failures. If the potential number of seeds is
fixed by the morphology of the plant, then a binomial distribution is
reasonable. If the potential number of seeds is dictated by
morphology, then I'd rather see it as counts and use a Poisson or
negative binomial.

The correct syntax in the binomial case is cbind(success, failure). Or
in your case cbind(seeds, 4 - seeds).

Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

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


2015-08-26 20:32 GMT+02:00 Mariano Devoto <mdevoto at agro.uba.ar>:
> Dear all. I am analysing data from a field experiment on a crop
> pollination. I want to test if there are differences in the number of seeds
> per fruit between three treatments. The experimental design consists of
> four separate sites where small subplots (ca. 5 plants each) received one
> of the treatments. In each site, 8 subplots were allocated to treatment A,
> 8 to treatment B and 4 to treatment C. When fruits were ripe I collected
> all plants from each subplot and counted stems, fruits per stem and seeds
> per fruit. I think a GLMM is the best way to go as I expect random effects
> related to field and subplot identity, and my response variable (number of
> seeds) is clearly non-normal. My main concern is the choice of the error
> family. As I’m counting seeds I first though of a Poisson model, but then
> realized that seed numbers only range from 0 to 4. I am now considering
> using a binomial model such as this:
>
>
> glmer(cbind(seeds,4) ~ treatment + (1|site) + (1|subplot), data=seed.data,
> family=binomial)
>
>
> Does this make sense?
>
>
> I would welcome any advice before hitting “SEND” in Tinn-R :-).
>
>
>
> --
> *Mariano Devoto*
>
>         [[alternative HTML version deleted]]
>
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