I am analyzing data from 3 field experiments (farms=3) for a citrus flower disease: response variable is binomial because the flower can only be diseased or healthy.
I have particular interest in comparing 5 fungicide spraying systems (trt=5). Each farm had 4 blocks (bk=4) including 2 trees as subsamples (tree=2) in which I assessed 100 flowers each one. This is a quick look of the data: farm trt bk tree dis tot <fctr> <fctr> <fctr> <fctr> <int> <int> iaras cal 1 1 0 100 iaras cal 1 2 1 100 iaras cal 2 1 1 100 iaras cal 2 2 3 100 iaras cal 3 1 0 100 iaras cal 3 2 5 100... The model I considered was: resp <- with(df, cbind(dis, tot-dis)) m1 = glmer(resp ~ trt + (1|farm/bk) , family = binomial, data=df) I tested the overdispersion with the overdisp_fun() from GLMM page <http://glmm.wikidot.com/faq> chisq ratio p logp 4.191645e+02 3.742540e+00 4.804126e-37 -8.362617e+01 As ratio (residual dev/residual df) > 1, and the p-value < 0.05, I considered to add the observation level random effect (link <http://r.789695.n4.nabble.com/Question-on-overdispersion-td3049898.html>) to deal with the overdispersion. farm trt bk tree dis tot tree_id <fctr> <fctr> <fctr> <fctr> <int> <int> <fctr> iaras cal 1 1 0 100 1 iaras cal 1 2 1 100 2 iaras cal 2 1 1 100 3... so now was added a random effect for each row (tree_id) to the model, but I am not sure of how to include it. This is my approach: m2 = glmer(resp ~ trt + (1|farm/bk) + (1|tree_id), family = binomial, data=df) I also wonder if farm should be a fixed effect, since it has only 3 levels... m3 = glmer(resp ~ trt * farm + (1|farm:bk) + (1|tree_id), family = binomial, data=df) I really appreciate your suggestions about my model specifications... *Juan​ Edwards- - - - - - - - - - - - - - - - - - - - - - - -# PhD student - ESALQ-USP/Brazil​* [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
