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

[Bert Gunter]

At this point, it seem obvious to me that you would benefit by local
statistical consulting, rather than further badgering on this list, as
you seem confused by both the underlying statistical concepts and how
they need to be handled in R/car. Pursuing your current course seems
destined to lead to folly.

Of course, both you and John (and others) are free to disagree ...

Cheers,
Bert



Bert Gunter

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
   -- Clifford Stoll


On Wed, Nov 25, 2015 at 7:04 PM, angelo.arcadi at virgilio.it
<angelo.arcadi at virgilio.it> wrote:
>
>
> 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
>>>
>>>
>>>
>>>
>>
>>
>
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