Re: [R] pmvt problem in multcomp

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From: Torsten Hothorn (Torsten.Hothorn@rzmail.uni-erlangen.de)
Date: Thu 27 May 2004 - 20:08:45 EST


Message-id: <Pine.LNX.4.51.0405271205330.1100@artemis.imbe.med.uni-erlangen.de>


>
> BTW, I have another strange example of simtest. I want to know
> why simtest returns these p-values.
>
> -- example 1 -------------------------------
> rm(list = ls())
> require(multcomp)
> y1 <- c(seq(3,7),seq(3,7))
> y2 <- c(rep(c(6,7,8,9),7))
> sort(runif(28),index=T) -> a
> y3 <- numeric(0)
> for(i in 1:28){
> y3[i] <- y2[a$ix[i]]
> }
> y4 <- c(y1,y3,14,18)
>
> f2 <- factor(c(rep(1,10),rep(2,8),rep(3,8),rep(4,8),rep(5,6)))
> dat2 <- cbind(as.data.frame(y4),f2)
> summary(simtest(y4 ~ f2, data=dat2, type="Dunnett"))
>
> > dat2
> y4 f2
> 1 3 1
> 2 4 1
> 3 5 1
> 4 6 1
> 5 7 1
> 6 3 1
> 7 4 1
> 8 5 1
> 9 6 1
> 10 7 1
> 11 6 2
> 12 7 2
> 13 6 2
> 14 9 2
> 15 7 2
> 16 8 2
> 17 6 2
> 18 8 2
> 19 9 3
> 20 8 3
> 21 7 3
> 22 9 3
> 23 6 3
> 24 8 3
> 25 9 3
> 26 7 3
> 27 7 4
> 28 9 4
> 29 6 4
> 30 6 4
> 31 9 4
> 32 8 4
> 33 7 4
> 34 9 4
> 35 6 5
> 36 8 5
> 37 8 5
> 38 7 5
> 39 14 5
> 40 18 5
> > summary(simtest(y4 ~ f2, data=dat2, type="Dunnett"))
>
> Simultaneous tests: Dunnett contrasts
>
> Call:
> simtest.formula(formula = y4 ~ f2, data = dat2, type = "Dunnett")
>
> Dunnett contrasts for factor f2
>
> Contrast matrix:
> f21 f22 f23 f24 f25
> f22-f21 0 -1 1 0 0 0
> f23-f21 0 -1 0 1 0 0
> f24-f21 0 -1 0 0 1 0
> f25-f21 0 -1 0 0 0 1
>
>
> Absolute Error Tolerance: 0.001
>
> Coefficients:
> Estimate t value Std.Err. p raw p Bonf p adj
> f25-f21 5.167 -4.644 1.022 0.000 0.000 0.000
> f23-f21 2.875 -2.813 1.022 0.008 0.024 0.022
> f24-f21 2.625 -2.569 1.022 0.015 0.029 0.028
> f22-f21 2.125 -2.079 1.113 0.045 0.045 0.045
> ---------------------------------
>
> I got the following inequality from the appended chart of a
> book.
>

hm, without knowing what

> 2.558 < d(5, 35, 0.4263464, 0.05) < 2.598

means it is hard to tell what the problem is. Could you please explain it
further?

Best,

Torsten

>
> Are these "p adj" values right?
> Or do I misunderstand some?
> --
> kuroki
> GnuPG fingerprint = 90FD FE79 905F 26F9 29C4 096F 8AA2 2C42 5130 1469
>
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>

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