title: Errors trying to run glmer with paired data and repeated measures (lme4)
body: <p>I want to analyze the effect of 2 treatments on the variation of the abundance of a plant species along a time gradient.</p>
  
  <p>The experimental design consist of exclosures (treatment = no moose), paired with control plots (treatment = moose). A site consist of 1 exclosure + 1 control plot. There are 15 sites (so 15 exclosures + 15 paired plots = 30 experimental units). Each experimental units has is unique "id". The abundance (proportion : continuous value between 0 and 1) of fir has been monitored for 5 years (once every year = repeated measures). So the repeated measures is nested inside the "id".</p>
  
  <p>I want to analyze the effect of treatments on fir abundance while controlling for the paired structure of the data and the repeated measures.</p>
  
  <p>Since the response data is a proportion (abundance between 0 and 1), I have been directed toward GLMM with family=binomial.</p>
  
  <p>However, I am not entirely sure on how to code my model. I tried :</p>
  
  <pre><code>fit = glmer(fir ~ treatment*time + (time|id) + (1|site), data=dat1, family=binomial)
  </code></pre>
  
  <p>If I get this right, "(1|site)" would control for the paired structure, and "(time|id)" would control for the repeated structure (since "time" is nested into "id").</p>
  
  <p>but I receive the following errors :</p>
  
  <pre><code>Warning messages:
  1: In eval(family$initialize, rho) :
  non-integer #successes in a binomial glm!
  2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
  unable to evaluate scaled gradient
  3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
  Hessian is numerically singular: parameters are not uniquely determined
  </code></pre>
  
  <p>Any idea what goes wrong with my model and what these error messages mean ?</p>
  
  <p>Thx </p>