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 <abedim...@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.onkel...@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 <abedim...@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.onkel...@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 <mdev...@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@r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> >> >> >> _______________________________________________ >> >> R-sig-ecology mailing list >> >> R-sig-ecology@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.ab...@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.ab...@modares.ac.ir > > Homepage > > Tel: +98-122-6253101 > > Fax: +98-122-6253499 _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology