[R] split plot design with missing plots

[Martin Henry H. Stevens]

Windows 2000 . 5.00.2195 with Service Pack 1.
R 1.5.1
Output from my split-split plot aov "alerted" me that I have done something 
wrong. I designed an experiment with all combinations of all levels of each 
treatment, but lost a little data (3 out of 192 plots). With the following 
data, I run the following model:

 > collim[c(1:6,187:192),c(1,3:6,9)]
              plot Litter Fert Seed  S density
X192.4  192      R   16    C  7      12
X192.3  192      C   16    C 14      26
X192.2  192      C   16    A  8       3
X192.1  192      R   16    A  9      12
X191.4  191      R   32    A  3       0
X191.3  191      C   32    A 10      11
.....
X146.2  146      R   32    C  7       7
X146.1  146      C   32    C  7       3
X145.4  145      R    8    C  9      21
X145.3  145      C    8    C  6      15
X145.2  145      R    8    A  9      10
X145.1  145      C    8    A  8      14

fm1 <- (log(S) ~ Fert*Seed*Litter*density+ Error(plot/Seed)

where Fertilizer is applied to entire plots, Seed is applied at two 
densities to nested subplots, and dead plant Litter is removed or not from 
sub-subplots within each Seed subplot. Variables plot, Fert, Seed, and 
Litter are factors, density and S (number of species present) are continuous.
The missing plots: 2 that received 16 g fertilizer, no seeds, and litter 
intact, 1 plot received no fertilizer, seeds added, and litter intact.

The output, below, tests All factors over Error: Within. I don't 
understand. I expected Fert to be tested over plot residuals, Seed and 
Seed:Fert tested over plot:Seed residuals, and all else tested over Within 
residuals.

Can any body help?

summary(fmc)

Error: plot
      Df  Sum Sq Mean Sq
Fert  1 0.98913 0.98913

Error: plot:Seed
      Df  Sum Sq Mean Sq
Fert  1 0.02016 0.02016

Error: Within
                           Df  Sum Sq Mean Sq F value    Pr(>F)
Fert                       3 16.0269  5.3423 59.2169 < 2.2e-16 ***
Seed                       1  0.0052  0.0052  0.0579   0.81009
Litter                     1  0.0834  0.0834  0.9242   0.33787
density                    1  5.0877  5.0877 56.3953  4.38e-12 ***
Fert:Seed                  3  0.0203  0.0068  0.0750   0.97336
Fert:Litter                3  0.0984  0.0328  0.3637   0.77930
Fert:density               3  0.7831  0.2610  2.8933   0.03719 *
Seed:Litter                1  0.0132  0.0132  0.1468   0.70217
Seed:density               1  0.0343  0.0343  0.3805   0.53826
Litter:density             1  0.2995  0.2995  3.3198   0.07038 .
Fert:Seed:Litter           3  0.0431  0.0144  0.1592   0.92361
Fert:Seed:density          3  0.9942  0.3314  3.6734   0.01359 *
Fert:Litter:density        3  0.3865  0.1288  1.4280   0.23674
Seed:Litter:density        1  0.0040  0.0040  0.0440   0.83410
Fert:Seed:Litter:density   3  0.1477  0.0492  0.5457   0.65175
Residuals                155 13.9834  0.0902
---


Martin Henry H. Stevens, Assistant Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056

Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
http://www.muohio.edu/~botcwis/bot/henry.html

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