Re: [R] F values from a Repeated Measures aov

From: John Vokey <>
Date: Tue, 29 Apr 2008 09:52:28 -0600

Two things:
1. the + Sex term is superfluous
2. the variable Subject needs to be a Factor, not a vector (as I suspect it currently is). That is, add:$Subject=as.factor($Subject)

in the preamble before the aov call, and all should be fine.

On 29-Apr-08, at 4:00 AM, wrote:

> Hi Folks,
> I have repeated measures for data on association time (under 2
> acoustic condtions) in male and female frogs as they grow to adulthood
> (6 timepoints). Thus, two within-subject variables (Acoustic
> Condition: 2 levels, Timepoint: 6 levels) and one between-subject
> variable (Sex:male or female).
> I am pretty sure my distributions depart from normality but I would
> first like to simply run a RM anova on the data. My problem is that
> when I do this I generate different values of F for my main effects
> and interaction when I do the analysis in [R] and SPSS - so I don't
> know which one to believe.
> Here is my code in R:
>>"mydata.txt", header=T) #read in my data
>>$Timepoint=as.factor($Timepoint) #col headings
> are factors so df are correct
>> aov.F=aov(Targ.Assoc.Time~(Timepoint*Acx.Cond*Sex) + Error(Subject/
>> (Timepoint*Acx.Cond))+(Sex),
> #run aov where i look at the main effects of Timepoint, Acoustic
> Condition and Sex as well as all the interactions therein on the
> amount of time a frog spends associating with the target sound.
> Include anything to do with Subject in the error term.
> Does this look right for a Repeated Measures ANOVA, or am I missing
> something to make it RM and that explains the large discrepancies in
> my F-values between [R] and SPSS?
> As soon as I get this canonical aov code figured out I want to derive
> my p-values by bootstrapping my F distributions, but first I need
> those canonical F's.
> Thanks
> -Alex
> --
> Alexander T Baugh
> Section of Integrative Biology
> Univ. of Texas at Austin C0930
> Austin, TX 78712

Please avoid sending me Word or PowerPoint attachments.
See <>

-Dr. John R. Vokey

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