[R] simtest for Dunnett's test

Fri Aug 13 14:37:52 CEST 2004

> Yes, but my control group is not always in the first colonne.
> So, I can have to a matrix like this:
> 1  0  0  -1  0
> 0  1  0  -1  0
> 0  0  1  -1  0
> 0  0  0  -1  0
>

see the `base' argument to `contrMat'.

Torsten

> Laurent Houdusse
> Analyste Programmeur
>
>
>
> -----Message d'origine-----
> De : Torsten Hothorn [mailto:Torsten.Hothorn at rzmail.uni-erlangen.de]
> Envoyé : vendredi 13 août 2004 14:19
> À : Liaw, Andy; Laurent Houdusse
> Cc : 'r-help at stat.math.ethz.ch'
> Objet : RE: [R] simtest for Dunnett's test
>
>
>
> On Fri, 13 Aug 2004, Liaw, Andy wrote:
>
> > Before you do any of that, you should realize the fact that simtest
> > does _not_ do Dunnett's test:  It can use `Dunnett' _contrasts_ to do
> > comparisons with a control, but the actual procedure is different.
> > You are unlikely to get the same result as other packages that perform
> > standard Dunnett's test (or Tukey's, for that matter).
> >
>
> exactly. btw, you don't need to specify the contrast matrix yourself for
> this type of question:
>
> R> summary(simtest(y ~ h))
>
>          Simultaneous tests: Dunnett contrasts
>
> Call:
> simtest.formula(formula = y ~ h)
>
>          Dunnett contrasts for factor h
>
> <...>
>
> Absolute Error Tolerance:  0.001
>
> Coefficients:
>        Estimate t value Std.Err. p raw p Bonf p adj
> h11-h1   12.022  -5.272     2.28 0.000  0.000 0.000
> h7-h1    11.556  -5.067     2.28 0.000  0.000 0.000
> h8-h1    10.952  -4.803     2.28 0.000  0.000 0.000
> h2-h1    10.414  -4.567     2.28 0.000  0.000 0.000
> h10-h1   10.247  -4.493     2.28 0.000  0.000 0.000
> h9-h1     9.494  -4.163     2.28 0.000  0.000 0.000
> h3-h1     7.397  -3.244     2.28 0.002  0.006 0.006
> h4-h1     5.384  -2.361     2.28 0.020  0.061 0.053
> h5-h1     5.085  -2.230     2.28 0.028  0.061 0.053
> h6-h1     3.180  -1.394     2.28 0.166  0.166 0.166
>
> does exactly the same because the `type' argument defaults to `Dunnett'.
>
> Best,
>
> Torsten
>
> > Andy
> >
> > > From: Laurent Houdusse
> > >
> > > Hi!
> > >
> > > I use simtest fonction of multcomp package to compile a Dunnett's
> > > test. I have 10 treatments and one control group, so i create a
> > > matrix with:
> > >
> > > m<-matrix(0,10,11)
> > > m[1,1]<--1
> > > m[1,2]<-1
> > > m[2,1]<--1
> > > m[2,3]<-1
> > > m[3,1]<--1
> > > m[3,4]<-1
> > > m[4,1]<--1
> > > m[4,5]<-1
> > > m[5,1]<--1
> > > m[5,6]<-1
> > > m[6,1]<--1
> > > m[6,7]<-1
> > > m[7,1]<--1
> > > m[7,8]<-1
> > > m[8,1]<--1
> > > m[8,9]<-1
> > > m[9,1]<--1
> > > m[9,10]<-1
> > > m[10,1]<--1
> > > m[10,11]<-1
> > > rownames(m)<-c("vehicle+vehicle vs. morphne
> > > 60mg/kg+vehicle","vehicle+vehicle vs. Naloxone
> > > 30mg/kg+vehicle","vehicle+vehicle vs. Naloxone 30mg/kg+Morphine
> > > 60mg/kg","vehicle+vehicle vs. RWJ-69528-000-B
> > > 0.1mg/kg+vehicle","vehicle+vehicle vs. RWJ-69528-000-B
> > > 1mg/kg+vehicle","vehicle+vehicle vs. RWJ-69528-000-B
> > > 0.1mg/kg+morphine 60mg/kg","vehicle+vehicle vs. RWJ-69528-000-B
> > > 1mg/kg+morphine 60mg/kg","vehicle+vehicle vs. vehicle+acetaminophen
> > > 600mg/kg","vehicle+vehicle vs. RWJ-69528-000-B
> > > 0.1mg/kg+acetaminophen 600mg/kg","vehicle+vehicle vs.
> > > RWJ-69528-000-B 1mg/kg+acetaminophen
> > > 600mg/kg")
> > > y<-c(21.5,14.7,16.7,18.8,17.3,15.527,17.551,17.199,15.895,14.3
> > > 88,30,30,30,21
> > > .2,14.6,30.83,30.622,30.465,24.563,31.416,30,30,30,30,19.6,17.
> > > 61,30.346,20.8
> > > ,17.045,18.129,17.9,15.4,30,15.9,22.9,31.909,25.633,24.6,20.35
> > > 5,18.807,30,18
> > > .9,16.4,18.2,22.3,21.3,28.571,17.357,16.983,30.40,26.3,24.4,25
> > > ,24.1,14.4,10.
> > > 256,13.266,29.6,15.344,18.69,30,30,25.7,30,28.5,30,30.32,30,19
> > > .879,30.716,25
> > > .2,30,30,30,30,30,14.063,28.811,30.396,30.609,30,14.1,30,30,30
> > > ,26.322,30.386
> > > ,28.583,15.77,29.341,30,17.1,30,30,30,30,20.451,30,23.967,30.5
> > > 07,30,30,30,27
> > > .7,30,28.5,22.568,32.379,30.374,28.263)
> > > h<-factor(c(rep(1:11, each = 10)))
> > > result<-summary(simtest(y ~ h,cmatrix=cbind(0,m)))
> > > rownames(result$estimate)
> > > result
> > >
> > >
> > > I want to compare my results with the results obtained with
> > > SigmaStat Software. In my results, i retrieve a correct q' value
> > > with the simtest t value How can i say if P<0.05 like the SigmStat
> > > results? Can i use p raw value, p bonf value, p adj value or other
> > > to compare directly? Or can i use the Dunnett's tables?
> > >
> > > Thanks for your help!
> > >
> > >
> > >
> > >
> > > Laurent Houdusse
> > > Analyste Programmeur
> > >
> > > ______________________________________________
> > > R-help at stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide!
> > > http://www.R-project.org/posting-guide.html
> > >
> > >
> >
> > ______________________________________________
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> >
> >
>
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