[R-sig-eco] nested factor for which i would like a parameter estimate

[dougwyu]

Hello all,

I am trying to test whether "sound diversity" predicts "bird diversity."  

The question i have concerns how to deal with a factor that could be treated either as a random or fixed factor.

Response:  bird_entropy (continuous)
Fixed factors:   landtype (factor), sound_entropy (continuous), AM/PM (factor)
Random factor:  Plot

The problematic factor is AM/PM.  

We have 29 total sampling plots, each of which is measured for sound_diversity at five subplots, once in the AM (dawn) and again in the PM (dusk), for a total 10 measurements per plot.  (Each plot has only one, overall measure of bird_diversity).  

On the one hand, AMPM is nested within plot, but on the other hand, we would like to estimate a parameter for AMPM, since we expect different suites of sound producers (not just birds) at different times of the day. However, it's reasonable to expect temporal correlation between AM and PM. 


The first model seems uncontroversial to me (these are post-model-selection).  

Mod.lme1 <- lme(bird_entropy ~ sound_entropy * landuse, random = ~ 1 | plot / AMPM, data=Bird) 


But i'm curious to know if this second model is reasonable, and if so, how would I code the plot variable?  

Mod.lme2 <- lme(bird_entropy ~ sound_entropy * landuse + AMPM, random = ~ 1 | plot, data=Bird)



Thanks all,

Doug