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 <istaz...@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 > <sergios...@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 <j...@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-boun...@r-project.org [mailto:r-help-boun...@r-project.org] >>> On >>>> Behalf Of Sergios (Sergey) Charntikov >>>> Sent: November-09-09 7:13 PM >>>> To: Mike Lawrence >>>> Cc: r-help@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.lawre...@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 >>>> > <sergios...@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.lawre...@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 >>>> > >> <sergios...@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@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@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 > ______________________________________________ R-help@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.