[R] Tukey HSD (or other post hoc tests) following repeated measures ANOVA

From: Ullrich Ecker <ullrich.ecker_at_uwa.edu.au>
Date: Wed, 28 May 2008 17:08:57 +0800

Hi everyone,

I am fairly new to R, and I am aware that others have had this problem before, but I have failed to solve the problem from previous replies I found in the archives.

As this is such a standard procedure in psychological science, there must be an elegant solution to this...I think.

I would much appreciate a solution that even I could understand... ;-)

Now, I want to calculate a post-hoc test following up a within-subjects ANOVA.

The dv is reaction time (RT), there is a 3-level Condition factor (Cond; within-subjects), a number of subjects (Subj), and the dataframe is called WMU3C.

The model is

> RT.aov <- aov(RT~Cond + Error(Subj/Cond), WMU3C)

I understand that TukeyHSD only works with an aov object, but that RT.aov is an aovlist object.

> class(RT.aov)

[1] "aovlist" "listof"

I've tried to work around it using the "maiz" example in the MMC documentation of the HH package (a solution previously recommended), but I couldn't get it to work: My best shot was to calculate another aov avoiding the error term (I don't see how this could be a feasible approach, but that's how I understood the MMC example) and a contrast vector (contrasting conditions 2 and 3):

I have to admit that I don't quite understand what I'm doing here (not that you couldn't tell)

> RT2.aov <- aov(terms(RT~Subj*Cond, WMU3C))
> Cond.lmat <- c(0,1,-1)
> Tukey <- glht.mmc(RT2.aov, focus = "Cond", focus.lmat = Cond.lmat)


Error in mvt(lower = carg$lower, upper = carg$upper, df = df, corr = carg$corr, :

   NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message:
In cov2cor(covm) : diagonal has non-finite entries

> Tukey


Thank you very much for your help!


Dr Ullrich Ecker
Postdoctoral Research Associate
Cognitive Science Laboratories
School of Psychology (Mailbag M304)
Room 211 Sanders Building
University of Western Australia
35 Stirling Hwy
Crawley WA 6009
Office: +61 8 6488 3266
Mobile: +61 4 5822 0072
Fax: +61 8 6488 1006
E-mail: ullrich.ecker_at_uwa.edu.au
Web: www.cogsciwa.com

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