[R] Getting Sphericity Tests for Within Subject Repeated Measure Anova (using "car" package) (Adjusted Dataset)

[Peter Dalgaard]

Sergios (Sergey) Charntikov wrote:
> Based on what you suggested I did the following:
> 
> 
> 1. Dataset$Sessn <- as.factor(Dataset$Sessn)
> 2. mod <- lm(cbind(Sessn=="1", Sessn=="2") ~ Trtmt, data=Dataset)
> 3. idata <- data.frame(Sessn=factor(1:2))
> 4. Anova(mod, idata=idata, idesign=~Sessn))
> ERROR:  The error SSP matrix is apparently of deficient rank = 0 < 1
> 
> I have noticed that my DV (Response) is not in play in the coding above.
> Then I have modified it to:
> 
> mod2 <- lm(*Response*~(cbind(Sessn=="1", Sessn=="2")) * Trtmt, data=Dataset)
> idata2 <- data.frame(Sessn=factor(1:2))
> Anova(mod, idata=idata2, idesign=~Sessn)
> ERROR: The error SSP matrix is apparently of deficient rank = 0 < 1
> 
> Then I have modified it to:
> 
> mod2 <- lm(Response~(cbind(Sessn=="1", Sessn=="2")) * Trtmt, data=Dataset)
> idata2 <- data.frame(Sessn=factor(1:2))
> Anova(mod, idata=idata2, idesign=~*(cbind(Sessn=="1", Sessn=="2")) * Trtmt*)
> ERROR:  object 'Trtmt' not found
> 
> Then I have modified it to:
> 
> mod2 <- lm(Response~(cbind(Sessn=="1", Sessn=="2")) * Trtmt, data=Dataset)
> idata2 <- data.frame(Sessn=factor(1:2))
> Anova(mod, idata=idata2, idesign=~(cbind(Sessn=="1", Sessn=="2")) * *
> Dataset$Trtmt*)
> ERROR:  variable lengths differ (found for 'Dataset$Trtmt') [THIS IS THE
> ERROR THAT I HAVE BEEN
> GETTING WITH MY ACTUAL DATASET FOLLOWING "CAR" PACKAGE RECOMMENDATIONS)


> Any idea what am I doing wrong?  I have attached my mock data for
> convenience in csv.

Either you forgot, or your mailer did not say that it is a text file, 
and the mailing list software consequently scrubbed it...

I think what you need is an analysis of 6 observations with a 
2x2==4-dimensional response. You may want to look at my paper in R News 
2007-2. The reacttime example used there is pretty similar. You're not 
going to get much sphericity testing when all factors have only two 
levels, though.

> 
> Sincerely,
> 
> Sergios Charntikov (Sergey), MA
> 
> Behavioral Neuropharmacology Lab
> Department of Psychology
> University of Nebraska-Lincoln
> Lincoln, NE 68588-0308  USA
> 
> sergioschr at gmail.com
> www.unl.edu/psychoneuropharm/
> 
> 
> On Mon, Nov 9, 2009 at 12:33 PM, John Fox <jfox at mcmaster.ca> wrote:
> 
>> Dear Segios,
>>
>> For repeated-measures designs, the Anova() function requires a multivariate
>> linear model fit to the "wide" version of the data set, in which each of
>> the
>> repeated measures appears as a separate variable. It is necessary that you
>> have the same occasions observed for all subjects. For your scaled-down
>> example, you'd have two response variables named, e.g., Sessn1 and Sessn2.
>> Then you'd fit the multivariate linear model as mod <- lm(cbind(Sessn1,
>> Sessn2) ~ Trtmnt, data=Dataset). The idata data frame could simply be idata
>> <- data.frame(Sessn=factor(1:2)). Then you could get the MANOVA and
>> repeated-measure ANOVA, including sphericity test, etc., as
>> summary(Anova(mod, idata=idata, idesign=~Sessn)).
>>
>> I hope this helps,
>>  John
>>
>> --------------------------------
>> John Fox
>> Senator William McMaster
>>  Professor of Social Statistics
>> Department of Sociology
>> McMaster University
>> Hamilton, Ontario, Canada
>> web: socserv.mcmaster.ca/jfox
>>
>>
>>> -----Original Message-----
>>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
>> On
>>> Behalf Of Sergios (Sergey) Charntikov
>>> Sent: November-09-09 1:18 PM
>>> To: r-help at r-project.org
>>> Subject: [R] Getting Sphericity Tests for Within Subject Repeated Measure
>>> Anova (using "car" package) (Adjusted Dataset)
>>>
>>> [corrected dataset below]
>>>
>>>
>>> Hello everyone,
>>>
>>> I am trying to do within subjects repeated measures anova followed by the
>>> test of sphericity (sample dataset below).
>>> I am able to get either mixed model or linear model anova and TukeyHSD,
>> but
>>> have no luck with Repeated-Measures Assuming Sphericity or Separate
>>> Sphericity Tests.
>>> I am trying to follow example from "car" package, but it seems that I am
>> not
>>> getting something right.
>>>
>>>> Dataset$Sessn <- as.factor(Dataset$Sessn)
>>>> LinearModel.1 <- lm(Response ~ Sessn*Trtmt, data=Dataset)
>>>> summary(LinearModel.1)
>>> All, good so far, but I have problem understanding "idata=" and
>> "idesign="
>>> functions pertaining to my example.  Session is my repeated measure
>> (Sessn
>> 1
>>> and Sessn 2 = two sessions, in reality I have more) and it is already
>>> stacked. Any help or guidance on this matter.
>>>
>>> Thank you, my mock dataset is below.  Each subject has two levels of
>>> treatment throughout four calendar days which are recoded to Session 1
>> and
>>> Session 2 in order to compare treatments by the first and subsequent days
>> of
>>> exposure (Treatment x Session; my DV is Response; Session is repeated).
>>>
>>> Subj      Trtmt      Sessn      Response
>>> 1     N     1     5
>>> 1     D     1     6
>>> 1     N     2     4
>>> 1     D     2     7
>>> 2     N     1     8
>>> 2     D     1     9
>>> 2     N     2     2
>>> 2     D     2     1
>>> 3     N     1     4
>>> 3     D     1     5
>>> 3     N     2     6
>>> 3     D     2     2
>>> 4     N     1     5
>>> 4     D     1     6
>>> 4     N     2     4
>>> 4     D     2     7
>>> 5     N     1     8
>>> 5     D     1     9
>>> 5     N     2     2
>>> 5     D     2     1
>>> 6     N     1     4
>>> 6     D     1     5
>>> 6     N     2     6
>>> 6     D     2     2
>>>
>>>
>>>
>>> Sincerely,
>>>
>>> Sergios Charntikov (Sergey), MA
>>>
>>> Behavioral Neuropharmacology Lab
>>> Department of Psychology
>>> University of Nebraska-Lincoln
>>> Lincoln, NE 68588-0308  USA
>>>
>>> sergioschr-at-gmail-dot-com
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
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>>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.


-- 
    O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
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