Hi Chris and Chris,
I was keeping my eye on this thread as I have also been discovering multiple comparisons recently. Your instructions are very clear! Thanks.
Now I would love to see an R boffin write a nifty function to produce a graphical representation of the multiple comparison, like this one:
http://www.theses.ulaval.ca/2003/21026/21026024.jpg
Should not be too difficult.....[any one up for the challenge?]
I came across more multiple comparison info here;
http://www.agr.kuleuven.ac.be/vakken/statisticsbyR/ANOVAbyRr/multiplecomp.htm
Cheers,
Sander.
Christoph Buser wrote:
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 <[EMAIL PROTECTED]> 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
> [EMAIL PROTECTED]
> > ______________________________________________
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-- -------------------------------------------- Dr Sander P. Oom Animal, Plant and Environmental Sciences, University of the Witwatersrand Private Bag 3, Wits 2050, South Africa Tel (work) +27 (0)11 717 64 04 Tel (home) +27 (0)18 297 44 51 Fax +27 (0)18 299 24 64 Email [EMAIL PROTECTED] Web www.oomvanlieshout.net/sander
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