[R-sig-ME] lme4 random effects for repeated measures, unbalanced data

[Ann Marie Raymondi]

Hello Listers,

I have a vegetation data set that consists of 150 plots that were sampled
1-3 times over a three year period.  Plots are my unit of observation and
they are unbalanced (since plots were sampled either once, twice, or three
times).  I would like to use mixed-effects models in order to account for
variation in both plots and sampling year and to keep my sample size large
(instead of conducting my analysis within individual years). Here is an
example of the grouping of my data:

Plot_ID       Plot     Year
2012_101   101     2012
2013_101   101     2013
2014_101   101     2014
2012_201   201     2012
2013_201   201     2013
2013_301   301     2013

My response variables are cover of vegetation functional groups and
predictors include variables related to fire and treatment history.
Additionally, I am not interested in how plots change over time per se, but
rather, in aggregating sampling from all three years to increase my sample
size and to account for the spatial/temporal correlation that arises from
doing so.  It is my assumption that treating plot as a random effect
(intercept only) accounts for variation that arises from potential spatial
autocorrelation, but my main question is how to account for the repeated
measures and if I need to account for the grouping of cells within sampling
years:

Potential model:

model<-lmer(response~covariates + (1|Plot) + (1|Year).

However, I know that is not appropriate to use a random effect with only
three levels, year in this case.  I'm hoping for recommendations on how to
incorporate year as a random effect.  Is including (Year |  Plot)
 recommended?  And if so, how might I interpret that effect, i.e., is it
accounting for variation introduced by different sampling year or variation
in plots over sampling year?

Thank you in advance for any help/suggestions!

Ann Marie

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