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

Ista Zahn istazahn at gmail.com
Tue Nov 10 04:53:32 CET 2009 

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

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