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