ANOVA 1 too few degrees of freedom

Thanks slre,

I seem to be making some progress now.

Using a colon instead of an asterisk in the code really changes things. I
had been getting residual SS and MS of zero. Which is ridiculous. Now I get
much more plausible values. 

Also, When I used an asterisk instead of a colon It wouldn't give results
for three way interactions. With colons it will.

You are correct about plot being nested within treatment. There are six
plots in each of 2 treatments.

So, I guess I will have to perform a separate analysis to quantify the
effect of treatment.

Beware that as you have highly significant effects of plot and its interaction with day, and plot being nested in treatment, you can't test for treatment or treatment:day effect with a systematic effect of plot  and plot:treatment in the model (you are only getting p values because of the sequential computation of the anova table - if you put plot before treatment, you'd get zero df). More likely, you want to make the "plot" terms random, as in ~treatment*day + Error(plot/day)
Thanks again.

Analysis of Variance Table

Response: Combined.Rs

Df  Sum Sq   Mean Sq   F value          Pr(>F)    
Combined.Trt                                                             1  
52.80     52.805     96.2601       < 2.2e-16 ***
Combined.Plot                                                            10 
677.69   67.769     123.5380    < 2.2e-16 ***
as.factor(Combined.Day)                                            16 
2817.47 176.092   321.0041    < 2.2e-16 ***
Combined.Trt:as.factor(Combined.Day)                      16   47.82    
2.989       5.4487        4.048e-10 ***
Combined.Trt:Combined.Plot:as.factor(Combined.Day)80  455.42   5.693      
10.3776      < 2.2e-16 ***
Residuals                                                                   
284 155.79   0.549                       
---
Signif. codes:  0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 

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ANOVA 1 too few degrees of freedom

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