From: kjetil halvorsen [mailto:kjetilh at umsanet.edu.bo]
Martin Hoyle wrote:
Dear Greg,
Thanks for the new release. The decomposition of the SSQ is
just what I need!
I thought decomposition of the SSQ can be obtained with the split=
argument to summary.aov? That argument seems tro be new --- it didnt
exist two years ago, and I was reacently made aware of it.
It might not be well known?
You are correct that summary.aov(...,split=..) is the method to get the SSQ
decompositions for analysis of variance contrasts.
The gregmisc package provides some functions useful for creating
(make.contrasts) and estimating (contrasts.lm) specific contrasts. I belive
that Martin was pleased with the example I provided in the make.contrasts
help page of using aov(...,contrasts=make.contrasts(...)) and
summary.aov(...,splits=...) to get the SSQ decompositions for the contrasts
he is interested in.
FWIW, too was unaware of the split argument to aov until a week or so ago.
I imagine that many people also unfamiliar with it. So, I'll paste my
example here just to give it more publicity, :-)
library(gregmisc)
Loading required package: MASS
Attaching package `gregmisc':
The following object(s) are masked from package:base :
lowess
# Create example data set with two factors: Genotype and Time
set.seed(03215)
Genotype <- sample(c("WT","KO"), 1000, replace=TRUE)
Time <- factor(sample(1:3, 1000, replace=TRUE))
y <- rnorm(1000)
data <- data.frame(y, Genotype, as.factor(Time))
cm.G <- rbind("KO vs WT"=c(-1,1) )
cm.T <- rbind("1 vs 2"=c(-1,1,0),
+ "2 vs 3"=c(0,-1,1) )
# Compute contrasts and show SSQ decompositions
model <- aov( y ~ Genotype + Time + Genotype:Time, data=data,
summary(model, split=list( Genotype=list( "KO vs WT"=1 ),
+ Time = list( "1 vs 2" = 1,
+ "2 vs 3" = 2 ) ) )
Df Sum Sq Mean Sq F value Pr(>F)
Genotype 1 0.0005446 0.0005446 0.0005 0.9814
Genotype: KO vs WT 1 0.0005446 0.0005446 0.0005 0.9814
Time 2 0.03 0.01 0.0141 0.9860
Time: 1 vs 2 1 0.03 0.03 0.0259 0.8722
Time: 2 vs 3 1 0.0023370 0.0023370 0.0023 0.9614
Genotype:Time 2 3.20 1.60 1.6032 0.2018
Genotype:Time: KO vs WT.1 vs 2 1 2.59 2.59 2.5900 0.1079
Genotype:Time: KO vs WT.2 vs 3 1 0.62 0.62 0.6163 0.4326
Residuals 994 992.39 1.00
-Greg
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