[R] Regarding aov Error()

Spencer Graves
Sun, 19 Mar 2006 18:04:41 -0000

Dear Prof. Vokey:

	  I can't answer your question regarding aov, because I never use it.
Instead, I use lme in library(nlme), which should be able to handle your
specific question and many more that aov can NOT handle.  I could get
your error message, but I don't know how to fix it using aov.

	  However, the following lme call looks like it might answer the
question you are asking:

 > library(nlme)
 > testNest <- lme(dv~Q,
+     random=list(s=~1, P=~1), data=testnest)
 > testNest
Linear mixed-effects model fit by REML
   Data: testnest
   Log-restricted-likelihood: -47.54548
   Fixed: dv ~ Q
(Intercept)         Qq2
       2.125       0.125

Random effects:
  Formula: ~1 | s
          (Intercept)
StdDev: 4.726742e-05

  Formula: ~1 | P %in% s
         (Intercept)    Residual
StdDev:    1.076244 0.005591059

Number of Observations: 32
Number of Groups:
        s P %in% s
        8       32

	  For me, the essential reference for lme is Pinheiro and Bates (2000)
Mixed-Effects Models in S and S-Plus (Springer).  Bates is perhaps the
leading contributor in this area, and I believe you will be amply
rewarded for appropriate study of this book.

	  hope this helps,
	  spencer graves

John Vokey wrote:

> The following dummy data frame has factor Q (with 2 levels) nesting
> factor P (with levels p1 and p2 nested under q1, and p3 and p4 nested
> under q2), but both crossing the random variate s, which has 8
> levels.  The dependent measure is dv.
>  > # The data frame:
>  > testnest
>     dv  s  P  Q
> 1   1 s1 p1 q1
> 2   2 s2 p1 q1
> 3   1 s3 p1 q1
> 4   2 s4 p1 q1
> 5   1 s5 p1 q1
> 6   3 s6 p1 q1
> 7   3 s7 p1 q1
> 8   4 s8 p1 q1
> 9   2 s1 p2 q1
> 10  3 s2 p2 q1
> 11  3 s3 p2 q1
> 12  1 s4 p2 q1
> 13  1 s5 p2 q1
> 14  2 s6 p2 q1
> 15  2 s7 p2 q1
> 16  3 s8 p2 q1
> 17  3 s1 p3 q2
> 18  3 s2 p3 q2
> 19  4 s3 p3 q2
> 20  1 s4 p3 q2
> 21  1 s5 p3 q2
> 22  1 s6 p3 q2
> 23  2 s7 p3 q2
> 24  2 s8 p3 q2
> 25  4 s1 p4 q2
> 26  3 s2 p4 q2
> 27  1 s3 p4 q2
> 28  2 s4 p4 q2
> 29  4 s5 p4 q2
> 30  1 s6 p4 q2
> 31  3 s7 p4 q2
> 32  1 s8 p4 q2
>
> # The following aov() call is structurally correct with respect
> # to the design, and appropriate error-terms, but, as can be seen,
> # returns an error:
>
>  > testnest.aov=aov(dv~Q+P%in%Q+Error(s+s:Q+s:P:Q),data=testnest)
> Warning message:
> Error() model is singular in: aov(dv ~ Q + P %in% Q + Error(s + s:Q +
> s:P:Q), data = testnest)
>
> # However, applying the summary() method to the aov output, produces
> the correct analysis:
>
>  > summary(testnest.aov)
>
> Error: s
>            Df Sum Sq Mean Sq F value Pr(>F)
> Residuals  7 5.8750  0.8393
>
> Error: s:Q
>            Df  Sum Sq Mean Sq F value Pr(>F)
> Q          1  0.1250  0.1250   0.068 0.8018
> Residuals  7 12.8750  1.8393
>
> Error: s:Q:P
>            Df Sum Sq Mean Sq F value Pr(>F)
> Q:P        2  0.250   0.125  0.1111 0.8956
> Residuals 14 15.750   1.125
>
> I have tried many different ways of denoting the Error()
> partitioning, but can't find one that produces both the correct
> analysis *AND* no singularity error on the aov() call.  Any suggestions?
>
> --
> Please avoid sending me Word or PowerPoint attachments.
> See <http://www.gnu.org/philosophy/no-word-attachments.html>
>
> -Dr. John R. Vokey
>
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