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

Sergios (Sergey) Charntikov sergioschr at gmail.com
Tue Nov 10 05:35:11 CET 2009


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





On Mon, Nov 9, 2009 at 9:53 PM, Ista Zahn <istazahn at gmail.com> wrote:
> 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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