Most likely your combined.trt is linearly dependent on the combined.plot
factor.  Try

Anova.Trt.D.M.T.Pr.Model <- aov(Combined.Rs ~  as.factor(Combined.Plot)
.....
and see if combined.plot now has the 11 df you are anticipating.

Rich

On Tue, May 3, 2011 at 3:37 PM, Rovinpiper <david.j.meehan@gmail.com> wrote:

> I'm running an ANOVA on some data for respiration in a forest. I am having
> a
> problem with my degrees of freedom. For one of my variables I get one fewer
> degrees of freedom than I should.
>
> I have 12 plots and I therefore expected 11 degrees of freedom, but instead
> I got 10.
>
> Any ideas?
>
> I have some code and output below:
>
>
> > class(Combined.Plot)
> [1] "character"
>
> > levels(as.factor(Combined.Plot))
>  [1] "60m"  "A1"   "B1"   "B3"   "B4"   "C5"   "C9"   "D2"   "D9"   "F60m"
> "F8"   "Q7"
>
> > nlevels(as.factor(Combined.Plot))
> [1] 12
>
> > Anova.Trt.D.M.T.Pr.Model <- aov(Combined.Rs~Combined.Trt +
> > as.factor(Combined.Plot) + as.factor(Combined.Day) +
> > Combined.Trt*as.factor(Combined.Day) +
> > Combined.Plot*as.factor(Combined.Day))
>
> Warning message:
> In model.matrix.default(mt, mf, contrasts) :
>  variable 'Combined.Plot' converted to a factor
>
> > summary(Anova.Trt.D.M.T.Pr.Model)
>                                                               Df  Sum Sq
> Mean Sq    F value           Pr(>F)
>
> Combined.Trt                                           1   52.80
> 52.805     2.0186e+30  < 2.2e-16 ***
> as.factor(Combined.Plot)                         10  677.69    67.769
> 2.5907e+30  < 2.2e-16 ***
> as.factor(Combined.Day)                         16  2817.47  176.092
> 6.7317e+30  < 2.2e-16 ***
> Combined.Trt:as.factor(Combined.Day)   16   47.82      2.989
> 1.1426e+29  < 2.2e-16 ***
> as.factor(Combined.Day):Combined.Plot 160  611.21   3.820 1.4604e+29 <
> 2.2e-16 ***
>
> Residuals                                                 204    0.00
> 0.000
>
> ---
>
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/ANOVA-1-too-few-degrees-of-freedom-tp3493349p3493349.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

	[[alternative HTML version deleted]]

