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: [email protected] [mailto:[email protected]] On > Behalf Of Sergios (Sergey) Charntikov > Sent: November-09-09 7:13 PM > To: Mike Lawrence > Cc: [email protected] > 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 <[email protected]> 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 > > <[email protected]> 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 <[email protected]> > 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 > > >> <[email protected]> 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]] > > >> > > > >> > ______________________________________________ > > >> > [email protected] 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. ~ ______________________________________________ [email protected] 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.
