Thank you for this example.

The way to handle it is with the split argument to the summary.aov function.
Look at ?summary.aov for details.

I use the reshape package to get the data ordered the way aov wants it.
I use the HH package for the graph.


## from:    Lundrigan, Cyril <cyrillundrig@gov.nl.ca>
## to:      r-help@r-project.org
## date:    Thu, May 9, 2013 at 7:58 AM
## subject: [R] Paritioning of Interaction SS in ANOVA - Gomez and
Gomez(1984) example

## Statistical Procedures in Agricultural Research, by K. A. Gomez and A.
A. Gomez. New York,
## Chichester, etc.: Wiley (1984).
## http://pdf.usaid.gov/pdf_docs/PNAAR208.pdf.


## Table 6.14 Data on Nitrogen Content of the Soil, Subjected to Eight
## Fertilizer Treatments In a RCB Design with Four Replications,
## Collected at Three Growth Stages of the Rice Crop

## Soil Nitrogen Content, %
## Treatment Rep. I   Rep. II  Rep. III Rep. IV
## Number    P1 P2 P3 P2 P2 P3 P1 P2 P3 P1 P2 P3

library(reshape)
library(HH)

GG614.in <- read.table(textConnection("
1 3.26 1.88 1.40 2.98 1.74 1.24 2.78 1.76 1.44 2.77 2.00 1.25
2 3.84 2.36 1.53 3.74 2.14 1.21 3.09 1.75 1.28 3.36 1.57 1.17
3 3.50 2.20 1.33 3.49 2.28 1.54 3.03 2.48 1.46 3.36 2.47 1.41
4 3.43 2.32 1.61 3.45 2.33 1.33 2.81 2.16 1.40 3.32 1.99 1.12
5 3.43 1.98 1.11 3.24 1.70 1.25 3.45 1.78 1.39 3.09 1.74 1.20
6 3.68 2.01 1.26 3.24 2.33 1.44 2.84 2.22 1.12 2.91 2.00 1.24
7 2.97 2.66 1.87 2.90 2.74 1.81 2.92 2.67 1.31 2.42 2.98 1.56
8 3.11 2.53 1.76 3.04 2.22 1.28 3.20 2.61 1.23 2.81 2.22 1.29
"))
closeAllConnections()

names(GG614.in) <- c("Treatment",
                     "I.P1", "I.P2", "I.P3", "II.P1", "II.P2", "II.P3",
                     "III.P1", "III.P2", "III.P3", "IV.P1", "IV.P2",
"IV.P3")

GG614 <- melt(GG614.in, id=1)
GG614$Rep <- rep(c("I","II","III","IV"), each=24)
GG614$GrowthStage <- factor(rep(c("P1","P2","P3"), each=8, times=4))
names(GG614)[3] <- "Nitrogen"
GG614$Treatment <- factor(GG614$Treatment)
GG614

## plot the data
interaction2wt(Nitrogen ~ Rep/Treatment + Treatment*GrowthStage, data=GG614)
interaction2wt(Nitrogen ~ Treatment*GrowthStage, data=GG614, simple=TRUE)

## Table 6.16
GG614.aov <- aov(Nitrogen ~ Error(Rep/Treatment) + Treatment*GrowthStage,
data=GG614)
summary(GG614.aov)

Treatment.contrasts <-
  ## 1 2 3 4 5 6 7 8
  cbind("7-1234568" = c( 1, 1, 1, 1, 1, 1,-7, 1),
        "8-123456"  = c( 1, 1, 1, 1, 1, 1, 0,-6),
        "25-1346"   = c(-1, 2,-1,-1, 2,-1, 0, 0),
        "2-5"       = c( 0, 1, 0, 0,-1, 0, 0, 0))

contrasts(GG614$Treatment)
contrasts(GG614$Treatment) <- Treatment.contrasts
contrasts(GG614$Treatment)

## Table 6.18
GG614.aov <- aov(Nitrogen ~ Error(Rep/Treatment) + Treatment*GrowthStage,
data=GG614)

summary(GG614.aov, expand.split=FALSE,
        split=list(Treatment=list(
                     "7-1234568"=1,
                     "8-123456"=2,
                     "25-1346"=3,
                     "2-5"=4,
                     rest=c(5,6,7)),
          "Treatment:GrowthStage"=list(
                     "7-1234568:P"=c(1,8),
                     "8-123456:P"=c(2,9),
                     "25-1346:P"=c(3,10),
                     "2-5:P"=c(4,11),
                     "rest:P"=c(5,6,7,12,13,14))
            ))





On Thu, May 9, 2013 at 7:58 AM, Lundrigan, Cyril <cyrillundrig@gov.nl.ca>wrote:

> Hello
> I'm a new user of R and I'm using Deducer as the interface but also
> making use of the command interface where necessary.  I'm trying to
> replicate Table 6.18 on page 262 in Statistical Procedures in
> Agricultural Research, by K. A. Gomez and A. A. Gomez. New York,
> Chichester, etc.: Wiley (1984).
> http://pdf.usaid.gov/pdf_docs/PNAAR208.pdf.  This example is highly
> relevant to the type of data we will be analyzing in our department but
> nobody here has experience doing partitioning of interactions with
> software.
>
> I've managed to replicate all previous steps for that particular
> exercise up to this point. If I interpret the syntax correctly, the
> table is showing comparisons of specific treatment combinations within
> the time variable P. Is this the correct interpretation?  If so, I don't
> know how to achieve that with R.  I had initially used SYSTAT for this
> exercise and had sent the problem along to their support person and
> after a few days the response was that he did not understand the syntax
> and, thus, could not replicate the table results. Unfortunately, it's
> also one of the few Gomez and Gomez examples not covered in the
> "agridat" package. I was trying to do the partiioning with
> interactionMeans and testInteractions functions in phia package but made
> no headway.  Greatly appreciate any help or direction with this.
>
>  Thanks!
>
>
>
>
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