[R] aov and missing values

[Peter Dalgaard BSA]

"Pedro J. Aphalo" <pedro.aphalo at joensuu.fi> writes:

> I am learning R, and although I have looked in the documentation, I may
> be asking something obvious. Sorry, if that is the case. 
> 
> In a split-plot design if there is a missing subunit summary gives me a
> table with two rows for the same factor, one in the error within section
> and one in the section using error between units. With no data missing
> the table is "normal". How does one interpret the table when data is
> missing?, or is it that aov cannot cope with missing values in this
> case?
> 
> Thanks in advance for any help.
> 
> Pedro.
> 
> The model I am using is of the form "y ~ A * B * C + block +
> Error(A/B)", I tried the simpler model "y ~ A * B + block + Error(A)"
> with the same result.

As a general matter, the theory for these designs is based on having
balanced data. The analysis with aov is based on an orthogonal
decompostion according to the error terms, which in the balanced case
means splitting into averages and differences of the values within a plot.
If each plot has received the same treatments, then there is no information
in the averages of the effect of treatment (and therefore it does not
appear in the between-unit stratum), but there will be if the
plots have received different sets of treatment. This will be the case
if some plots have missing values, but not only that: The error model
also becomes dubious (it essentially implies that averages have the same
variance no matter how many observations they are averages of). 

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
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