[R] Q about how to use Anova.mlm

John Fox jfox at mcmaster.ca
Fri Jan 30 03:42:56 CET 2009


Dear Paul,

I noticed a typo in my response and some poor formatting in the email
message; please see below:

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
> Behalf Of John Fox
> Sent: January-29-09 9:23 PM
> To: 'pgseye'
> Cc: r-help at r-project.org
> Subject: Re: [R] Q about how to use Anova.mlm
> 
> Dear Paul,
> 
> First, to fit a multivariate linear model to your data, you'll have to
> rearrange the data from "long" format (with one observation per replicate)
> to "wide" format (with one observation per subject). If your data are in
the
> data frame Data, then you'd do something like:
> 
> Wide <- reshape(Data, v.names="Angle", idvar="Subject",
timevar="Replicate",
> direction="wide")
> 
> Then, with the data in wide format, fit a multivariate linear model with
> just a constant:
> 
> mod <- lm(cbind(Angle.1, Angle.2, Angle.3, Angle.4, Angle.5, Angle.6) ~ 1,
> data=DavisThin)

The data argument should be data=Wide (I adapted the code from an example I
already had and neglected to change the argument).

> 
> Finally, use Anova() to get the tests:
> 
> idata <- data.frame(Replicate=c("Angle.1", "Angle.2", "Angle.3",
"Angle.4",
> "Angle.5", "Angle.6"))
> summary(Anova(mod, idata=idata, idesign=~Replicate))

Note that this is indeed two separate commands; they were apparently run
together by my mailer.

Regards,
 John

> 
> If I understand correctly what you want, this should give it to you.
> 
> As well, since your design has no between-subject factors and only a
single
> within-subject factor, you could also use anova() [i.e., anova.mlm()] to
get
> the same results.
> 
> I hope this helps,
>  John
> 
> ------------------------------
> John Fox, Professor
> Department of Sociology
> McMaster University
> Hamilton, Ontario, Canada
> web: socserv.mcmaster.ca/jfox
> 
> 
> > -----Original Message-----
> > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
> On
> > Behalf Of pgseye
> > Sent: January-29-09 7:40 PM
> > To: r-help at r-project.org
> > Subject: [R] Q about how to use Anova.mlm
> >
> >
> > Hi,
> >
> > Am newish to stats and R, so I certainly appreciate any help. Basically
I
> > have 50 inidividuals whom I have 6 photos each of their optic nerve
head.
> I
> > want to check that the orientation of the nerve head is consistent, ie
the
> 6
> > replicates show minimal or preferably no rotation differences. I'll draw
> an
> > arbitrary line between some blood vessels (same reference in each set of
> > replicates) and determine an angle of deviation from the vertical and
that
> > angle will be my dependent variable.
> >
> > Subject	  Replicate	  Angle of Deviation
> > 1		       1		       x
> > 1		       2		       x
> > 1		       3		       x
> > 1		       4		       x
> > 1		       5		       x
> > 1		       6		       x
> > 2		       1		       x
> > 2		       2		       x
> > 2		       3		       x
> > 2		       4		       x
> > 2		       5		       x
> > 2		       6		       x
> > etc
> >
> > I'm wanting to test for Sphericity (because I've read that you should -
is
> > this routine in a repeated measures ANOVA?) and can see that Anova.mlm
in
> > the CAR package offers this in addition to the alternative Greenhouse
and
> > Feldt tests.
> >
> > I just don't really know how to perform the test - can someone give me
> some
> > help.
> >
> > Thank you.
> >
> > Paul
> >
> > Dept of Ophthalmology
> > Uni Melbourne, Australia
> > --
> > View this message in context: http://www.nabble.com/Q-about-how-to-use-
> > Anova.mlm-tp21739443p21739443.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > ______________________________________________
> > 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.
> 
> ______________________________________________
> 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.



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