[R] R: Re: R: RE: Syntax error in using Anova (car package)
angelo.arcadi at virgilio.it
angelo.arcadi at virgilio.it
Thu Nov 26 10:33:00 CET 2015
Dear Bert,
I do not have any statistical consultant that I can find near me or pay. Yes,
I was confused by some statistical
concept, but I remember you, with humility, that human beings have the
possibility to learn. Some even
learn fast! Don't under estimate the will of a person of learning.
However, it is my hope that you are the only one that feels so much pissed off
by my HELP requests!
The point of a forum is to provide help, don't you think? And there might be
people in future that reading
my posts over internet can find solutions to the same problem. Do you know
that there are many
people around that do not have a statistical consultant available and try to
learn by themselves?
I do hope that some one could provide an answer to my last question, since it
is just a syntactical question
and this is the most appropriate forum in the world that can help me (and
maybe others in future) in
understanding and solving the problem.
Thank you
Best regards
Angelo
>----Messaggio originale----
>Da: bgunter.4567 at gmail.com
>Data: 26-nov-2015 3.24
>A: "angelo.arcadi at virgilio.it"<angelo.arcadi at virgilio.it>
>Cc: <jfox at mcmaster.ca>, "r-help at r-project.org"<r-help at r-project.org>
>Ogg: Re: [R] R: RE: Syntax error in using Anova (car package)
>
>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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