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

[Thierry Onkelinx]

Dear Mehdi,

Assuming that you want to model the probability of germination, yes.

Note that cbind(seed, 100) is WRONG syntax.
CORRECT syntax: cbind(n_success, n_failure)

Have you tried anova(your.model)?

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


2015-08-27 11:19 GMT+02:00 Mehdi Abedi <abedimail at gmail.com>:
> 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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>> > R-sig-ecology at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
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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
>
> Homepage
>
> Tel: +98-122-6253101
>
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