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

[Mehdi Abedi]

Dear Thierry and Mariano,

Could we apply these glmer for seed germination in petridishes which the
total number of seeds is defined as well? like  cbind(seeds,100).

 In addition what is the simple way to get ANOVA liked tables (i think with
Chisquare would be better test than F value) for these test with having P-
value as well?
Warm regards,
Mehdi

On Thu, Aug 27, 2015 at 12:20 PM, Thierry Onkelinx <thierry.onkelinx at inbo.be
> wrote:

> 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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>
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-- 


*Mehdi Abedi Department of Range Management*

*Faculty of Natural Resources & Marine Sciences *

*Tarbiat Modares University (TMU) *

*46417-76489, Noor*

*Mazandaran, IRAN *

*mehdi.abedi at modares.ac.ir <Mehdi.abedi at modares.ac.ir>*

*Homepage
<http://www.modares.ac.ir/en/Schools/nat/Academic_Staff/~mehdi.abedi>*

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