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

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]

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,

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

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

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

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]]

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]]

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]]