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

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Have you tried ezANOVA from the ez pacakge? It attempts to provide a
simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
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
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.

Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~
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No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca> wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide a
simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~
Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug in my levels, plug in my covariate (since it is all within) and
get my Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable 'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2, Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below.  Maybe I am not
coding it right? I would hate to recode all my data for SPSS, since at
the end I would need to show that Sphericity was not violated.

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
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca> wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide a
simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~
-------------- next part --------------
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
Dear Sergios,

Why don't you try what I suggested originally? Adapted to this data set,

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
idata <- data.frame(Day=factor(1:3))
summary(Anova(mod, idata=idata, idesign=~Day))

Peter Dalgaard also pointed toward an article that describes how to do the
same thing with anova().

Regards,
 John
-----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 7:13 PM
To: Mike Lawrence
Cc: r-help at r-project.org
Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
Measure
Anova (using "car" package)

Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug
in my levels, plug in my covariate (since it is all within) and get my
Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable
'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below.  Maybe I am not
coding
it right? I would hate to recode all my data for SPSS, since at the end I
would need to show that Sphericity was not violated.

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

On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide
a simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~
Thank you very much.  Finally got it to work.  However, I had to recode it from:
columns: subject/treatment/DV (where all my response data was in one
DV column) to columns: subject/treatment/day1/day2/day3/ (where my
response data is now in three different columns).

Is there a way to do that without hand recoding (cutting and pasting
in spreadsheet) by hand? Thank you for your help.  Glad it works as
is.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308  USA
Dear Sergios,

Why don't you try what I suggested originally? Adapted to this data set,

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
idata <- data.frame(Day=factor(1:3))
summary(Anova(mod, idata=idata, idesign=~Day))

Peter Dalgaard also pointed toward an article that describes how to do the
same thing with anova().

Regards,
?John

-----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 7:13 PM
To: Mike Lawrence
Cc: r-help at r-project.org
Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
Measure
Anova (using "car" package)

Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug
in my levels, plug in my covariate (since it is all within) and get my
Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable
'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below. ?Maybe I am not
coding
it right? I would hate to recode all my data for SPSS, since at the end I
would need to show that Sphericity was not violated.

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

On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide
a simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

Yes, reshaping data is straightforward in R. No need to copy/paste in
a spreadsheet.
See ?reshape and/or the melt/cast functions in the reshape package.

-Ista

On Mon, Nov 9, 2009 at 9:20 PM, Sergios (Sergey) Charntikov
Thank you very much. ?Finally got it to work. ?However, I had to recode it from:
columns: subject/treatment/DV (where all my response data was in one
DV column) to columns: subject/treatment/day1/day2/day3/ (where my
response data is now in three different columns).

Is there a way to do that without hand recoding (cutting and pasting
in spreadsheet) by hand? Thank you for your help. ?Glad it works as
is.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 7:12 PM, John Fox <jfox at mcmaster.ca> wrote:
Dear Sergios,

Why don't you try what I suggested originally? Adapted to this data set,

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
idata <- data.frame(Day=factor(1:3))
summary(Anova(mod, idata=idata, idesign=~Day))

Peter Dalgaard also pointed toward an article that describes how to do the
same thing with anova().

Regards,
?John

-----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 7:13 PM
To: Mike Lawrence
Cc: r-help at r-project.org
Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
Measure
Anova (using "car" package)

Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug
in my levels, plug in my covariate (since it is all within) and get my
Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable
'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below. ?Maybe I am not
coding
it right? I would hate to recode all my data for SPSS, since at the end I
would need to show that Sphericity was not violated.

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

On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide
a simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

______________________________________________
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.

Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
Thank you very much for all your help.  This helped a lot. Very
constructive input.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308  USA
Yes, reshaping data is straightforward in R. No need to copy/paste in
a spreadsheet.
See ?reshape and/or the melt/cast functions in the reshape package.

-Ista

On Mon, Nov 9, 2009 at 9:20 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Thank you very much. ?Finally got it to work. ?However, I had to recode it from:
columns: subject/treatment/DV (where all my response data was in one
DV column) to columns: subject/treatment/day1/day2/day3/ (where my
response data is now in three different columns).

Is there a way to do that without hand recoding (cutting and pasting
in spreadsheet) by hand? Thank you for your help. ?Glad it works as
is.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 7:12 PM, John Fox <jfox at mcmaster.ca> wrote:
Dear Sergios,

Why don't you try what I suggested originally? Adapted to this data set,

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
idata <- data.frame(Day=factor(1:3))
summary(Anova(mod, idata=idata, idesign=~Day))

Peter Dalgaard also pointed toward an article that describes how to do the
same thing with anova().

Regards,
?John

-----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 7:13 PM
To: Mike Lawrence
Cc: r-help at r-project.org
Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
Measure
Anova (using "car" package)

Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug
in my levels, plug in my covariate (since it is all within) and get my
Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable
'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below. ?Maybe I am not
coding
it right? I would hate to recode all my data for SPSS, since at the end I
would need to show that Sphericity was not violated.

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

On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide
a simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

______________________________________________
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.

--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

Check out the reshape package for transforming data from long to wide
and vice versa.

Yet I still don't know what problem you've encountered with ezANOVA.
Using the data you just sent, where Day now has 3 levels, I reformat
back to the presumably original long format and find that ezANOVA
returns the same sphericity tests as John's solution (which is
expected because ezANOVA is a wrapper to Anova):

library(ez)
a = read.table( 'Sergios_wide_data.txt' , header=T )
b = melt.data.frame( data=a , id.vars=c('subject','treatment') ,
variable_name='day' )
ezANOVA( data=b , dv=.(value) , sid=.(subject) , within=.(treatment,day) )

On Mon, Nov 9, 2009 at 10:20 PM, Sergios (Sergey) Charntikov
Thank you very much. ?Finally got it to work. ?However, I had to recode it from:
columns: subject/treatment/DV (where all my response data was in one
DV column) to columns: subject/treatment/day1/day2/day3/ (where my
response data is now in three different columns).

Is there a way to do that without hand recoding (cutting and pasting
in spreadsheet) by hand? Thank you for your help. ?Glad it works as
is.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 7:12 PM, John Fox <jfox at mcmaster.ca> wrote:
Dear Sergios,

Why don't you try what I suggested originally? Adapted to this data set,

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
idata <- data.frame(Day=factor(1:3))
summary(Anova(mod, idata=idata, idesign=~Day))

Peter Dalgaard also pointed toward an article that describes how to do the
same thing with anova().

Regards,
?John

-----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 7:13 PM
To: Mike Lawrence
Cc: r-help at r-project.org
Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
Measure
Anova (using "car" package)

Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug
in my levels, plug in my covariate (since it is all within) and get my
Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable
'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below. ?Maybe I am not
coding
it right? I would hate to recode all my data for SPSS, since at the end I
would need to show that Sphericity was not violated.

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

On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide
a simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~
Oops, I see now that despite repeated subject names, treatment is a
between-Ss variable, so you need to use this to get the equivalent of
Anova:

library(ez)
a = read.table( 'Sergios_wide_data.txt' , header=T )
b = melt.data.frame( data=a , id.vars=c('subject','treatment') ,
variable_name='day' )
b$subject=paste(b$subject,b$treatment) #create unique sids
ezANOVA( data=b , dv=.(value) , sid=.(subject) , within=.(day) ,
between=.(treatment) )
Check out the reshape package for transforming data from long to wide
and vice versa.

Yet I still don't know what problem you've encountered with ezANOVA.
Using the data you just sent, where Day now has 3 levels, I reformat
back to the presumably original long format and find that ezANOVA
returns the same sphericity tests as John's solution (which is
expected because ezANOVA is a wrapper to Anova):

library(ez)
a = read.table( 'Sergios_wide_data.txt' , header=T )
b = melt.data.frame( data=a , id.vars=c('subject','treatment') ,
variable_name='day' )
ezANOVA( data=b , dv=.(value) , sid=.(subject) , within=.(treatment,day) )

On Mon, Nov 9, 2009 at 10:20 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Thank you very much. ?Finally got it to work. ?However, I had to recode it from:
columns: subject/treatment/DV (where all my response data was in one
DV column) to columns: subject/treatment/day1/day2/day3/ (where my
response data is now in three different columns).

Is there a way to do that without hand recoding (cutting and pasting
in spreadsheet) by hand? Thank you for your help. ?Glad it works as
is.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 7:12 PM, John Fox <jfox at mcmaster.ca> wrote:
Dear Sergios,

Why don't you try what I suggested originally? Adapted to this data set,

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
idata <- data.frame(Day=factor(1:3))
summary(Anova(mod, idata=idata, idesign=~Day))

Peter Dalgaard also pointed toward an article that describes how to do the
same thing with anova().

Regards,
?John

-----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 7:13 PM
To: Mike Lawrence
Cc: r-help at r-project.org
Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
Measure
Anova (using "car" package)

Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug
in my levels, plug in my covariate (since it is all within) and get my
Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable
'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below. ?Maybe I am not
coding
it right? I would hate to recode all my data for SPSS, since at the end I
would need to show that Sphericity was not violated.

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

On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide
a simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~
Thank you.  I think that this is what I was looking for.  I am getting
the hang of it with my data.  Thank you all.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308  USA
Oops, I see now that despite repeated subject names, treatment is a
between-Ss variable, so you need to use this to get the equivalent of
Anova:

library(ez)
a = read.table( 'Sergios_wide_data.txt' , header=T )
b = melt.data.frame( data=a , id.vars=c('subject','treatment') ,
variable_name='day' )
b$subject=paste(b$subject,b$treatment) #create unique sids
ezANOVA( data=b , dv=.(value) , sid=.(subject) , within=.(day) ,
between=.(treatment) )

On Tue, Nov 10, 2009 at 6:47 AM, Mike Lawrence <Mike.Lawrence at dal.ca> wrote:
Check out the reshape package for transforming data from long to wide
and vice versa.

Yet I still don't know what problem you've encountered with ezANOVA.
Using the data you just sent, where Day now has 3 levels, I reformat
back to the presumably original long format and find that ezANOVA
returns the same sphericity tests as John's solution (which is
expected because ezANOVA is a wrapper to Anova):

library(ez)
a = read.table( 'Sergios_wide_data.txt' , header=T )
b = melt.data.frame( data=a , id.vars=c('subject','treatment') ,
variable_name='day' )
ezANOVA( data=b , dv=.(value) , sid=.(subject) , within=.(treatment,day) )

On Mon, Nov 9, 2009 at 10:20 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Thank you very much. ?Finally got it to work. ?However, I had to recode it from:
columns: subject/treatment/DV (where all my response data was in one
DV column) to columns: subject/treatment/day1/day2/day3/ (where my
response data is now in three different columns).

Is there a way to do that without hand recoding (cutting and pasting
in spreadsheet) by hand? Thank you for your help. ?Glad it works as
is.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 7:12 PM, John Fox <jfox at mcmaster.ca> wrote:
Dear Sergios,

Why don't you try what I suggested originally? Adapted to this data set,

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)
idata <- data.frame(Day=factor(1:3))
summary(Anova(mod, idata=idata, idesign=~Day))

Peter Dalgaard also pointed toward an article that describes how to do the
same thing with anova().

Regards,
?John

-----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 7:13 PM
To: Mike Lawrence
Cc: r-help at r-project.org
Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated
Measure
Anova (using "car" package)

Hi Mike,

I tried to run my data in SPSS and it works fine without any problems,
plug
in my levels, plug in my covariate (since it is all within) and get my
Mauchly Tests.

I tried to rearrange the data so it looks like this

subj/treatment/day1/day2/day3

subject??? treatment??? day1??? day2??? day3
1??? 1??? 8??? 8??? 8
1??? 2??? 5??? 7??? 5
2??? 1??? 7??? 4??? 4
2??? 2??? 4??? 5??? 7
3??? 1??? 8??? 6??? 4
3??? 2??? 5??? 2??? 4
4??? 1??? 2??? 9??? 4
4??? 2??? 1??? 9??? 1
5??? 1??? 4??? 8??? 1
5??? 2??? 7??? 8??? 2
6??? 1??? 4??? 7??? 2
6??? 2??? 4??? 5??? 2

When I try mlmfit <- lm(Dataset~1), I get "invalid type (list) for
variable
'Dataset"

When I try

mod <- lm(cbind(day1, day2, day3) ~ Treatment, data=Dataset)

idata<- data.frame(factor(rep(c(Dataset$day1, Dataset$day2,
Dataset$day3))),
ordered(Dataset$Treatment))

Anova(mod, idata=idata, idesign=~Dataset$Treatment)

I get: Terms in the intra-subject model matrix are not orthogonal.

When I try is.matrix(Dataset) - I get no.

My original mock Dataset (attached in txt) is below. ?Maybe I am not
coding
it right? I would hate to recode all my data for SPSS, since at the end I
would need to show that Sphericity was not violated.

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

On Mon, Nov 9, 2009 at 5:29 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
No luck as in...? What error did you encounter?

In your example data set, you only have 2 levels of each within-Ss
factor, in which case you shouldn't expect to obtain tests of
sphericity; as far as I understand it, sphericity necessarily holds
when for repeated measures with only 2 levels and tests are really
only possible for repeated measures with 3 or more levels.

I think it's analogous to how you don't need to test homogeneity of
variance when performing a paired t-test; the test ends up
representing the pairs as single distribution of difference scores
with a single variance.

Mike

On Mon, Nov 9, 2009 at 5:30 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
Tried EZanova, no luck with my particular dataset.

Sincerely,

Sergios Charntikov (Sergey), MA

Behavioral Neuropharmacology Lab
Department of Psychology
University of Nebraska-Lincoln
Lincoln, NE 68588-0308 ?USA

On Mon, Nov 9, 2009 at 2:25 PM, Mike Lawrence <Mike.Lawrence at dal.ca>
wrote:
Have you tried ezANOVA from the ez pacakge? It attempts to provide
a simple user interface to car's ANOVA (and when that fails, aov).

On Mon, Nov 9, 2009 at 1:44 PM, Sergios (Sergey) Charntikov
<sergioschr at gmail.com> wrote:
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
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.

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~

--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University

Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar

~ Certainty is folly... I think. ~