interaction and nested notation in lmer
On Mon, Sep 21, 2015 at 6:24 PM, Mashitah Jusoh <mashitahj at gmail.com> wrote:
Hi, I would like to ask about the notation to indicated nested and interaction when using lmer function. Here is my experiment look like: I have 95 genotypes with 2 replications that were conducted in two years. Some of the observation were missing, making the dataset unbalance. So, I decided to use lmer function to fit the data to get the variance component and will treat all components as random. The model that I am going to fit is: Y=mean + year + genotype + rep (nested in year) + genotype*year + error I am wondering how to write the command for nested and interaction term in R using lmer function for this model? As far as I search in the internet, the command for nested and interaction seems like using similar notation, for example (1|year:rep) to show rep is nested within year (for random effect) the same notation is used to indicate the interaction (for other variables, such as genotype:year). Correct me if i am wrong. And, can you give some clarification about this and also how lmer/ R works with interaction and nested data?
If you have samples from only 2 years, it's not going to be particularly practical to fit a model with year as random effect. Setting that aside for the moment, the distinction between (1|year/rep) and (1|year:rep) is that the former expands to (1|year) + (1|year:rep) (i.e., effect of year and effect of rep within year), while the latter is just rep within year -- i.e. no main effect of year. However, nesting syntax doesn't really doesn't work well for fixed effects (partly due to the way R handles the formulae, and partly for conceptual reasons) -- in your model, year:rep would give 4 fixed-effect parameters, as would year+rep+year:rep or year*rep (two ways of specifying crossed effects) I think I would recommend Y ~ 1 + year*rep + (1|genotype) + (1|genotype:year) With unbalanced data, it may be hard to get a unique decomposition of variance ... Ben Bolker