[R] drop1

[John Fox]

Dear Federico,

At 05:24 PM 10/2/2002 +0100, Federico Calboli wrote:
>Dear All,
>
>I was trying to reproduce prof. Venables analysis on Sheffe data for rats:
>
>http://www.stats.ox.ac.uk/pub/MASS3/Exegeses.pdf
>
>I have no problems concerning the aov side of the analysis, but I noticed
>that drop1 in R gives me a completely different result than those on the
>Exegeses. In particular my Sum of Squares and RSS are wildly different.
>
>I used :
>
> > drop1(aov.model1,.~.,test="F")
>
>Single term deletions
>
>Model:
>WT ~ Litter + Mother + Litter:Mother
>               Df Sum of Sq    RSS    AIC F value   Pr(F)
><none>                     2440.8  257.0
>Litter         3     591.7 3032.5  264.3  3.6362 0.01968 *
>Mother         3     582.3 3023.1  264.1  3.5782 0.02099 *
>Litter:Mother  9     824.1 3264.9  256.8  1.6881 0.12005
>
>which is pretty different form prof. Venables results:
>
>Model:
>Wt ˜ Litter * Mother
>         Df      Sum of Sq RSS   F Value         Pr(F)
><none>  2440.816
>Litter  3       27.6559 2468.472 0.169959 0.9161176
>Mother  3       671.7376 3112.554 4.128153 0.0114165
>Litter:Mother 9 824.0725 3264.889 1.688108 0.1200530
>
>Any suggestion why?

The default contrast type for unordered factors is different in S-Plus and 
R: In S-Plus it is contr.helmert; in R, contr.treatment. You can obtain the 
published results by, e.g., setting the contrast type explicitly:

     > mod.1 <- aov(Wt ~ Litter*Mother, data=genotype)
     > drop1(mod.1, .~., test="F")
     Single term deletions

     Model:
     Wt ~ Litter + Mother + Litter:Mother
                 Df Sum of Sq    RSS    AIC F value   Pr(F)
     <none>                     2440.8  257.0
     Litter         3     591.7 3032.5  264.3  3.6362 0.01968
     Mother         3     582.3 3023.1  264.1  3.5782 0.02099
     Litter:Mother  9     824.1 3264.9  256.8  1.6881 0.12005

     > mod.2 <- update(mod.1,
     +     contrasts=list(Litter=contr.helmert, Mother=contr.helmert))
     > drop1(mod.2, .~., test="F")
     Single term deletions

     Model:
     Wt ~ Litter + Mother + Litter:Mother
                 Df Sum of Sq    RSS    AIC F value   Pr(F)
     <none>                     2440.8  257.0
     Litter         3      27.7 2468.5  251.7  0.1700 0.91612
     Mother         3     671.7 3112.6  265.9  4.1282 0.01142
     Litter:Mother  9     824.1 3264.9  256.8  1.6881 0.12005

Regards,
  John

-----------------------------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario, Canada L8S 4M4
email: jfox at mcmaster.ca
phone: 905-525-9140x23604
web: www.socsci.mcmaster.ca/jfox
-----------------------------------------------------


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