R help - Feb 2000 - random effects in analysis of variance

I have a data.frame paint (below-mentioned). In SPlus I used the command 

raov( MOISTURE ~ BATCH / PROBE )

(you could do raov( MOISTURE ~ BATCH +  PROBE%in%BATCH) as well)

so that the factors are taken as random. In R this function raov doesn't
exist. How can I calculate the same? Maybe with lme, but how? 

str(paint)
----------
`data.frame':	60 obs. of  5 variables:
 $ BATCH   : Factor w/ 15 levels
"1","2","3","4",..: 1 1 1 1 2 2 2 2 3 3
...
 $ SAMPLE  : num  1 1 2 2 3 3 4 4 5 5 ...
 $ REP     : num  1 2 1 2 1 2 1 2 1 2 ...
 $ MOISTURE: num  40 39 30 30 26 28 25 26 29 28 ...
 $ PROBE   : Factor w/ 2 levels "1","2": 1 1 2 2 1 1 2 2 1 1
...

dput(paint)
-----------
structure(list(BATCH = structure(c(1, 1, 1, 1, 2, 2, 2, 2, 3, 
3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 
8, 8, 9, 9, 9, 9, 10, 10, 10, 10, 11, 11, 11, 11, 12, 12, 12, 
12, 13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15), .Label = c("1", 
"2", "3", "4", "5", "6",
"7", "8", "9", "10", "11",
"12", "13",
"14", "15"), class = "factor"), SAMPLE = c(1, 1,
2, 2, 3, 3,
4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 
13, 14, 14, 15, 15, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 
21, 22, 22, 23, 23, 24, 24, 25, 25, 26, 26, 27, 27, 28, 28, 29, 
29, 30, 30), REP = c(1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 
1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 
2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 
1, 2, 1, 2), MOISTURE = c(40, 39, 30, 30, 26, 28, 25, 26, 29, 
28, 14, 15, 30, 31, 24, 24, 19, 20, 17, 17, 33, 32, 26, 24, 23, 
24, 32, 33, 34, 34, 29, 29, 27, 27, 31, 31, 13, 16, 27, 24, 25, 
23, 25, 27, 29, 29, 31, 32, 19, 20, 29, 30, 23, 24, 25, 25, 39, 
37, 26, 28), PROBE = structure(c(1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 
2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 
2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 
1, 1, 2, 2, 1, 1, 2, 2), .Label = c("1", "2"), class =
"factor")), .Names = c("BATCH",
"SAMPLE", "REP", "MOISTURE", "PROBE"),
row.names = c("1", "2",
"3", "4", "5", "6", "7",
"8", "9", "10", "11", "12",
"13", "14",
"15", "16", "17", "18", "19",
"20", "21", "22", "23", "24",
"25",
"26", "27", "28", "29", "30",
"31", "32", "33", "34", "35",
"36",
"37", "38", "39", "40", "41",
"42", "43", "44", "45", "46",
"47",
"48", "49", "50", "51", "52",
"53", "54", "55", "56", "57",
"58",
"59", "60"), class = "data.frame")
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>>>>> "Monika" == Monika Ferster <ferster at
stat.math.ethz.ch> writes:
    Monika> I have a data.frame paint (below-mentioned). In SPlus I used
    Monika> the command raov( MOISTURE ~ BATCH / PROBE )

    Monika> (you could do raov( MOISTURE ~ BATCH + PROBE%in%BATCH) as well)

    Monika> so that the factors are taken as random. In R this function
    Monika> raov doesn't exist. How can I calculate the same? Maybe with
    Monika> lme, but how?

	    .....

sehr gut!
Ich hoffe, wir bekommen nützliche Antworten..

Martin
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On Thu, 10 Feb 2000, Monika Ferster wrote:
> I have a data.frame paint (below-mentioned). In SPlus I used the command 
> 
> raov( MOISTURE ~ BATCH / PROBE )
> 
> (you could do raov( MOISTURE ~ BATCH +  PROBE%in%BATCH) as well)
> 
> so that the factors are taken as random. In R this function raov
doesn't
> exist. How can I calculate the same? Maybe with lme, but how? 
Easier, in both S and R
> summary(aov( MOISTURE ~ BATCH + Error(BATCH / PROBE) , data=paint))
Error: BATCH 
      Df Sum of Sq  Mean Sq 
BATCH 14  1210.933 86.49524

Error: PROBE %in% BATCH 
          Df Sum of Sq  Mean Sq F Value Pr(F) 
Residuals 15    869.75 57.98333              

Error: Within 
          Df Sum of Sq   Mean Sq F Value Pr(F) 
Residuals 30      27.5 0.9166667              

but just so you know how,

fit <- lme(MOISTURE ~ 1, random = ~1 | BATCH / PROBE, data=paint)

is the fit you want, and print or summary will let you pick off the
estimates you might need.

There is a worked example almost exactly like this in V&R3.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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