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

[Sergios (Sergey) Charntikov]

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. ~
-------------- 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