[R] R: RE: Syntax error in using Anova (car package)

[angelo.arcadi at virgilio.it]

Dear Prof. John Fox, 
thanks a lot for your answer. Do you mean that my data set should have 19 rows 
(one for each of the 19 subjects)
and 144 columns (that is 72 trials * 2 dependent variables)? So should the 
dataframe look like this?

Subject     Stimulus_1.Centroid.repetition1  Stimulus_1.Centroid.repetition2 
Stimulus_1.Peak.repetition1  Stimulus_1.Peak.repetition2 
Subject1    1000                             2000                              
10                           20                
Subject2    500                              
600                                5                           6    
......
SubjectN


However, differently from the example reported in the document you kindly 
provided, my experiment
has two dependent variables. 
My guess is that the analysis should be the following (considering 12 types of 
stimuli and 6 repetitions 
for each of them, and 2 dependent variables)



stimulus_type <- factor(rep(c("Stimulus_1", "Stimulus_2", "Stimulus_3", 
"Stimulus_4", "Stimulus_5", "Stimulus_6", 
 "Stimulus_7", "Stimulus_8", "Stimulus_9", "Stimulus_10", "Stimulus_11", 
"Stimulus_12"), c(6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6)), 
levels=c("Stimulus_1", "Stimulus_2", "Stimulus_3", "Stimulus_4", "Stimulus_5", 
"Stimulus_6", 
 "Stimulus_7", "Stimulus_8", "Stimulus_9", "Stimulus_10", "Stimulus_11", 
"Stimulus_12"))
 
repetitions <- ordered(rep(1:6, 12))

idata <- data.frame(stimulus_type, repetitions)

Notably, now idata has 72 rows (should it have 144 rows instead?). Then I 
continue with:


mod.ok <- lm(cbind(Stimulus_1.Centroid.repetition1, ....., Stimulus_12.Peak.
repetition2) ~  Subject, data=scrd)

av.ok <- Anova(mod.ok, idata=idata, idesign=~stimulus_type*repetitions)


Am I correct?

Thanks in advance

Best regards

Angelo




>----Messaggio originale----
>Da: jfox at mcmaster.ca
>Data: 25-nov-2015 17.23
>A: "angelo.arcadi at virgilio.it"<angelo.arcadi at virgilio.it>
>Cc: "r-help at r-project.org"<r-help at r-project.org>
>Ogg: RE: Syntax error in using Anova (car package)
>
>Dear Angelo,
>
>I'm afraid that this is badly confused. To use Anova() for repeated measures, 
the data must be in "wide" format, with one row per subject. To see how this 
works, check out the OBrienKaiser example in ?Anova and ?OBrienKaiser, or for 
more detail, the R Journal paper at <{http://journal.r-project.org/archive/2013-
1/RJournal_2013-1_fox-friendly-weisberg.pdf>.
>
>I hope this helps,
> John
>
>-----------------------------------------------
>John Fox, Professor
>McMaster University
>Hamilton, Ontario, Canada
>http://socserv.socsci.mcmaster.ca/jfox/
>
>
>
>> -----Original Message-----
>> From: angelo.arcadi at virgilio.it [mailto:angelo.arcadi at virgilio.it]
>> Sent: Wednesday, November 25, 2015 11:30 AM
>> To: r-help at r-project.org
>> Cc: Fox, John
>> Subject: Syntax error in using Anova (car package)
>> 
>> Dear list members,
>> I am getting an error while performing a repeated measures MANOVA using
>> the Anova function
>> of the "car" package. I want to apply it on the results of an experiment
>> involving 19 participants,
>> who were subjected to 36 stimuli, each stimulus was repeated twice for a
>> total of 72 trials
>> per subject. Participants had to adjust two parameters of sounds,
>> Centroid and Sound_Level_Peak,
>> for each stimulus. This is the head of my dataset (dependent variables:
>> Centroid and
>> Sound_Level_Peak; independent variables: Mat (6 levels) and Sh (2
>> levels)).
>> 
>> > head(scrd)
>>     Subject         Mat   Sh      Centroid            Sound_Level_Peak
>> 1     Subject1      C     DS        1960.2               -20.963
>> 2     Subject1      C     SN        5317.2               -42.741
>> 3     Subject1      G     DS       11256.0               -16.480
>> 4     Subject1      G     SN        9560.3               -19.682
>> 5     Subject1      M     DS        4414.1               -33.723
>> 6     Subject1      M     SN        4946.1               -23.648
>> 
>> 
>> Based on my understanding of the online material I found, this is the
>> procedure I used:
>> 
>> idata <- data.frame(scrd$Subject)
>> mod.ok <- lm(cbind(Centroid,Sound_Level_Peak) ~  Mat*Sh,data=scrd)
>> av.ok <- Anova(mod.ok, idata=idata, idesign=~scrd$Subject)
>> 
>> 
>> I get the following error
>> 
>> Error in check.imatrix(X.design) :
>>   Terms in the intra-subject model matrix are not orthogonal.
>> 
>> 
>> Can anyone please tell me what is wrong in my formulas?
>> 
>> Thanks in advance
>> 
>> Best regards
>> 
>> Angelo
>> 
>> 
>> 
>> 
>
>