Hierarchical glm with binomial family
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'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
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