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 <mehdi.ab...@modares.ac.ir>* *Homepage <http://www.modares.ac.ir/en/Schools/nat/Academic_Staff/~mehdi.abedi>* *Tel: +98-122-6253101 * *Fax: +98-122-6253499* [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology