[R] Test for multiple comparisons: Nonlinear model, autocorrelation?

[J S]

Dear R community, 
 
I have a nonlinear model describing average daily soil temperature. What test 
should I use to compare differences in soil temperature of the two studied 
vegetation types depending upon month?
 
Building linear contrasts for the developed nonlinear model does not help since 
this model does not include variable “Months” (only “Days”). 
 
1) Just a Student’s test is not probably an option because I would violate an 
assumption of independency, since the daily soil temperature observations have 
high autocorrelation. Or maybe I could average the observations for each month 
and then use this test since I have observations for a few years, and it might 
overcome the problem of independency?
 
2) Should I develop a second nonlinear model with months instead of days, but 
it would considerably increase a number of parameters in the model...
 
Or:
3) ?
 
Thanks for your help,
Julia
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