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

[Sergios (Sergey) Charntikov]

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.


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]]
> >
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>
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