On Wed, May 27, 2009 at 9:17 AM, Ben Bolker <bol...@ufl.edu> wrote: > > > > Johan Stenberg-2 wrote: >> >> Dear members of the R help list, >> >> I want to do a hierarchical glm with binomial family but am unsure >> about how to write the syntax which involves nesting. >> >> I want to test whether the risk of being attacked by Herbivores for >> Meadowsweet plants is significantly dependent on the Distance to >> heterospecific source plants. >> >> Dependent variable = Herbivory (yes/no) >> Explanatory continuous variable = Distance to heterospecific source plant >> >> Distance should be nested within Subpopulation which in turn should be >> nested within Population. >> The number of replicates per subpopulation varies between 8 and 36. >> The number of subpopulations per population varies between 4 and 9. >> >> I haven't figured out how to do nesting, but guessing that nesting is >> denoted with brackets I guess the syntax should look something like >> this (below). Could you please help me to correct this syntax so that >> it becomes useful in R? >> >> model<-glm(Herbivory~Distance(Subpopulation(Population)), family=binomial) >> >> > > You probably need a GLMM (generalized linear mixed model), which is > a little bit of a can of worms. If so, you will need the "glmer" function > inside the "lmer" package.
I think you mean the lme4 package. > I'm not entirely clear about your experimental design: I understand > that subpopulations are nested within populations, but it's not clear > whether covariates (distances to heterospecific plants) differ within > subpopulations or populations. > > If they don't differ with subpopulations, I would (strongly) recommend > aggregating the > values within subpopulations and analyzing proportions as a regression > analysis: > see Murtaugh, Paul A. “SIMPLICITY AND COMPLEXITY IN ECOLOGICAL > DATA ANALYSIS.” Ecology 88, no. 1 (2007): 56-62. > > If they do, then your design is > > model<-glmer(Herbivory~Distance+(1|Population/Subpopulation), > family=binomial) > > See also: > > https://stat.ethz.ch/pipermail/r-sig-mixed-models/2009q2/002320.html > https://stat.ethz.ch/pipermail/r-sig-mixed-models/2009q2/002335.html > -- > View this message in context: > http://www.nabble.com/Hierarchical-glm-with-binomial-family-tp23742335p23743418.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
