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

Thu Aug 27 12:02:47 CEST 2015

You need to specify the models which you want to compare

model2<- glmer(cbind(germinated, Nongerminated) ~ temp * light +
(1|Replication), data= growthdata, family = binomial)
model2.bis <- glmer(cbind(germinated, Nongerminated) ~ temp + light +
(1|Replication), data= growthdata, family = binomial)
anova(model2, model2.bis)

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 11:57 GMT+02:00 Mehdi Abedi <abedimail at gmail.com>:
> 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
>
> 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
>
>
>
>
> --
>
> 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