[R] planned comparisons for ANOVA

[Simon Blomberg]

Darren Weber wrote:

[snip]
> Our planned comparisons are:
>
> 1. test the group mean difference for S1 vs S2 (in the absence of S3)
> 2. test the group mean difference for S2 vs S3 (in the absence of S1)
>
> This is the current form of the ANOVA specification for R:
>
> aov( Y ~ (Task*Hemisphere*Group) +
>                 Error( Subject/(Task*Hemisphere) )
>   
> How can we add planned comparisons to this specification?  Can we add
> just one planned comparison matrix, with rows for 1 & 2 above, or do
> we need to run the model twice, once for each planned comparison?
>   
There are a couple of ways to do this in R. Perhaps the easiest is to 
use make.contrasts in the gmodels package.

cmat <- rbind("S1 v S2" = c(1, -1, 0),
                      "S2 v S3" = c(0, 1, -1))
library(gmodels)
fit <- aov( Y ~ Task*Hemisphere*Group + Error( 
Subject/(Task*Hemisphere), contrasts=list("Task"=make.contrasts(cmat )))
summary(fit)

> Alternatively, is there a function  to compute the planned comparisons
> after running the full ANOVA model?
>   
see ?fit.contrast in gmodels  for this.

HTH,

Simon.
> Thanks, Darren
>
> PS, I was trained well on using SPSS, but I am trying to make a switch
> to R.  You help with this would be really appreciated.  We need to get
> our results revised and published soon.
>
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>   


-- 
Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat.
Centre for Resource and Environmental Studies
The Australian National University
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