I haven't been able to fully make sense of the conflicting online information about whether and how to specify nesting structure for a nested, mixed model. I'll describe my experiment and hopefully somebody who knows lme4 well can help.
We're measuring the fluorescence intensity of brain slices from frogs that have undergone various treatments. We want to use multcomp to look for differences between treatments, while accounting for the variance introduced by the random effects of brain and slice. There are a few measurements per slice, several slices per brain, and several brains per treatment. In the data file, the numbering for slices starts over from 1 for each brain, and the numbering for brains starts over from 1 for each treatment. In other words: Treatment is a fixed effect, brain is a random effect nested in treatment, and slice is a random effect nested in brain. As I understood the documentation, this is the correct specification: log(Intensity) ~ Treatment + (1|Brain) + (1|Slice) However, I don't see how lmer understands the correct nesting structure from that. How does it know brain isn't crossed with treatment? Here are two other things I tried, and each gave different results: log(Intensity) ~ Treatment + (1|Slice/Brain/Treatment) log(Intensity) ~ Treatment + (1|Brain/Treatment) + (1|Slice/Brain) I'm not sure why these things give different results, or which one (if any) is right. Can anyone help? Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Need-help-with-lmer-model-specification-syntax-for-nested-mixed-model-tp3020895p3020895.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.