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

[John Fox]

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. ~