Re: [R] adjusted p-values with TukeyHSD?

From: Christoph Strehblow <chrisxe_at_gmx.at>
Date: Tue 17 May 2005 - 21:47:10 EST

Hi!

Thanks a lot, works as advertised. If i used Tukey, it even gives raw, Bonferroni- and Tukey-corrected p-values!

Thx for the help,

Christoph Strehblow, MD
Department of Rheumatology, Diabetes and Endocrinology Wilhelminenspital, Vienna, Austria
chrisxe@gmx.at

Am 17.05.2005 um 13:23 schrieb Christoph Buser:

> Dear Christoph
>
> You can use the multcomp package. Please have a look at the
> following example:
>
> library(multcomp)
>
> The first two lines were already proposed by Erin Hodgess:
>
> summary(fm1 <- aov(breaks ~ wool + tension, data = warpbreaks))
> TukeyHSD(fm1, "tension", ordered = TRUE)
>
> Tukey multiple comparisons of means
> 95% family-wise confidence level
> factor levels have been ordered
>
> Fit: aov(formula = breaks ~ wool + tension, data = warpbreaks)
>
> $tension
> diff lwr upr
> M-H 4.722222 -4.6311985 14.07564
> L-H 14.722222 5.3688015 24.07564
> L-M 10.000000 0.6465793 19.35342
>
>
> By using the functions simtest or simint you can get the
> p-values, too:
>
> summary(simtest(breaks ~ wool + tension, data = warpbreaks,
> whichf="tension",
> type = "Tukey"))
>
> Simultaneous tests: Tukey contrasts
>
> Call:
> simtest.formula(formula = breaks ~ wool + tension, data = warpbreaks,
> whichf = "tension", type = "Tukey")
>
> Tukey contrasts for factor tension, covariable: wool
>
> Contrast matrix:
> tensionL tensionM tensionH
> tensionM-tensionL 0 0 -1 1 0
> tensionH-tensionL 0 0 -1 0 1
> tensionH-tensionM 0 0 0 -1 1
>
>
> Absolute Error Tolerance: 0.001
>
> Coefficients:
> Estimate t value Std.Err. p raw p Bonf p adj
> tensionH-tensionL -14.722 -3.802 3.872 0.000 0.001 0.001
> tensionM-tensionL -10.000 -2.582 3.872 0.013 0.026 0.024
> tensionH-tensionM -4.722 -1.219 3.872 0.228 0.228 0.228
>
>
>
> or if you prefer to get the confidence intervals, too, you can
> use:
>
> summary(simint(breaks ~ wool + tension, data = warpbreaks,
> whichf="tension",
> type = "Tukey"))
>
> Simultaneous 95% confidence intervals: Tukey contrasts
>
> Call:
> simint.formula(formula = breaks ~ wool + tension, data = warpbreaks,
> whichf = "tension", type = "Tukey")
>
> Tukey contrasts for factor tension, covariable: wool
>
> Contrast matrix:
> tensionL tensionM tensionH
> tensionM-tensionL 0 0 -1 1 0
> tensionH-tensionL 0 0 -1 0 1
> tensionH-tensionM 0 0 0 -1 1
>
> Absolute Error Tolerance: 0.001
>
> 95 % quantile: 2.415
>
> Coefficients:
> Estimate 2.5 % 97.5 % t value Std.Err. p raw p
> Bonf p adj
> tensionM-tensionL -10.000 -19.352 -0.648 -2.582 3.872 0.013
> 0.038 0.034
> tensionH-tensionL -14.722 -24.074 -5.370 -3.802 3.872 0.000
> 0.001 0.001
> tensionH-tensionM -4.722 -14.074 4.630 -1.219 3.872 0.228
> 0.685 0.447
>
> -----------------------------------------------------------------
> Please be careful: The resulting confidence intervals in
> simint are not associated with the p-values from 'simtest' as it
> is described in the help page of the two functions.
> -----------------------------------------------------------------
>
> I had not the time to check the differences in the function or
> read the references given on the help page.
> If you are interested in the function you can check those to
> find out which one you prefer.
>
> Best regards,
>
> Christoph Buser
>
> --------------------------------------------------------------
> Christoph Buser <buser@stat.math.ethz.ch>
> Seminar fuer Statistik, LEO C13
> ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
> phone: x-41-44-632-4673 fax: 632-1228
> http://stat.ethz.ch/~buser/
> --------------------------------------------------------------
>
>
> Christoph Strehblow writes:
>
>> hi list,
>>
>> i have to ask you again, having tried and searched for several
>> days...
>>
>> i want to do a TukeyHSD after an Anova, and want to get the adjusted
>> p-values after the Tukey Correction.
>> i found the p.adjust function, but it can only correct for "holm",
>> "hochberg", bonferroni", but not "Tukey".
>>
>> Is it not possbile to get adjusted p-values after Tukey-correction?
>>
>> sorry, if this is an often-answered-question, but i didnīt find it on
>> the list archive...
>>
>> thx a lot, list, Chris
>>
>>
>> Christoph Strehblow, MD
>> Department of Rheumatology, Diabetes and Endocrinology
>> Wilhelminenspital, Vienna, Austria
>> chrisxe@gmx.at
>>
>> ______________________________________________
>> R-help@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
>>
>
>



R-help@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 Received on Tue May 17 21:51:05 2005

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