generalized mixed models with proportion data using lme4

- Also, I realize I incorrectly cited p-values from glmer summary
tables (instead of those derived from, for example, LR tests); the
p-value for Treatment derived from the Likelihood Ratio test was
p=0.01, which is even more ambiguous, but my main points / questions
remain the same.

Have you done the permutation test within your pairs?  I think that 
answers your main question.

I don't see why you wish to go to repeated measures modelling of 
individual leaves, unless you think the distribution of damage might be 
different under the nets, in which case you would need an appropriate 
interaction term in the RE part.

Just 2c, David Duffy.

| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v