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

[Mehdi Abedi]

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

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

*Tel: +98-122-6253101 *

*Fax: +98-122-6253499*

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