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

Thu Aug 27 12:08:23 CEST 2015

On 27/08/15 11:57, Mehdi Abedi wrote:
> Dear Thierry,
> Yes i am using (success, failure) but in this case i need to change all
> data frame. I was thinking to use codes which is not necessary to create
> new column when you have a ll of species. Because we know
> success(germinated seeds) and we know failure (Total seeds -
> success(germinated seeds)).
>
> Yes i used codes with ANOVA but there is no P- value for study.
>
> model2<- glmer(cbind(germinated, Nongerminated) ~ temp *light +
> (1|Replication ), data=growthdata,
> + family=binomial)
>> anova(model2)
> Analysis of Variance Table
>             Df Sum Sq Mean Sq F value
> temp        2 30.600  15.300  15.300
> light       1 46.231  46.231  46.231
> temp:light  2 22.877  11.439  11.439
p-values are difficult. See here:
<http://glmm.wikidot.com/faq>

Better to stick to reporting your effect sizes: your analysis of 
deviance only tells you if you have enough data to see a difference, not 
how big the differences are.

Also, if Replication is 1:nrow(growthdata), you could use a simple GLM 
and estimate your over-dispersion term (the residual deviance divided by 
the residual sum of squares should be OK). You can use this to correct 
the standard errors with summary(glm.obj, dispersion=overdisp).

Bob

> Warm regards,
> Mehdi
>
>
> On Thu, Aug 27, 2015 at 1:56 PM, Thierry Onkelinx <thierry.onkelinx at inbo.be>
> wrote:
>
>> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-ecology mailing list
>>>>> R-sig-ecology at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>> _______________________________________________
>>>> R-sig-ecology mailing list
>>>> R-sig-ecology at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>
>>>
>>>
>>> --
>>>
>>> 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
>>>
>>> Fax: +98-122-6253499
>
>

-- 

Bob O'Hara

Biodiversity and Climate Research Centre
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Germany

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