From: Kjetil Brinchmann Halvorsen <kjetil_at_acelerate.com>

Date: Fri 25 Mar 2005 - 11:28:51 EST

Date: Fri 25 Mar 2005 - 11:28:51 EST

Kjetil Brinchmann Halvorsen wrote:

> Jason W. Martinez wrote:

*>
**>> Dear R-users,
**>>
**>> I have an outcome variable and I'm unsure about how to treat it. Any
**>> advice?
**>>
**> If you only concentrate on the relative proportions, this are called
**> compositional data. I f your data are in
**> mydata (n x 4), you obtain compositions by
**> sweep(mydata, 1, apply(mydata, 1, sum), "/")
**>
**> There are not (AFAIK) specific functions/packages for R for
**> compositional data AFAIK, but you
**> can try googling. Aitchison has a monography (Chapman & Hall) and a
**> paper in JRSS B.
**>
**> One way to start might be lm's or anova on the symmetric logratio
**> transform of the
**> compositons. The R function lm can take a multivariate response, but
**> some extra programming will be needed
**> for interpretation. With simulated data:
**>
**> > slr
**> function(y) { # y should sum to 1
**> v <- log(y)
**> return( v - mean(v) ) }
**> > testdata <- matrix( rgamma(120, 2,3), 30, 4)
**> > str(testdata)
**> num [1:30, 1:4] 0.200 0.414 0.311 2.145 0.233 ...
**> > comp <- sweep(testdata, 1, apply(testdata,1,sum), "/")
**> # To get the symmetric logratio transform:
**> comp <- t(apply(comp, 1, slr))
**> # Observe:
**> apply(cov(comp), 1, sum)
**> [1] -5.551115e-17 2.775558e-17 5.551115e-17 -2.775558e-17
**> > lm( comp ~ 1)
**>
**> Call:
**> lm(formula = comp ~ 1)
**>
**> Coefficients:
**> [,1] [,2] [,3] [,4] (Intercept)
**> 0.17606 0.06165 -0.03783 -0.19988
*

Followup:

> mmod <- manova(comp ~ x)

> summary(mmod)

Error in summary.manova(mmod) : residuals have rank 3 < 4
>

So the manova() function cannot be used. I guess MANOVA for
compositional data should be

a straight extension, but it must be programmed , standard manova cannot
be used.

Kjetil

-- Kjetil Halvorsen. Peace is the most effective weapon of mass construction. -- Mahdi Elmandjra -- No virus found in this outgoing message. Checked by AVG Anti-Virus. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.htmlReceived on Fri Mar 25 11:40:52 2005

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