Re: [R] Name for factor's levels with contr.sum

From: Christoph Buser <buser_at_stat.math.ethz.ch>
Date: Thu 14 Jul 2005 - 01:41:13 EST

Dear Ghislain

I do not know a general elegant solution, but for some applications the following example may be helpful:

## Artificial data for demonstration: group is fixed, species is random dat <- data.frame(group = c(rep("A",20),rep("B",17),rep("C",24)),

                  species = c(rep("sp1", 4), rep("sp2",5),   rep("sp3",5),
                    rep("sp4",6),  rep("sp5",2),  rep("sp6",5),  rep("sp7",3),
                    rep("sp8",3), rep("sp9",4), rep("sp10",6),  rep("sp11",6),
                    rep("sp12",6), rep("sp13",6)),
                  area = rnorm(61))

## You can attach a contrast at your fixed factor of interest "group"
## Create the contrast you like to test (in our case contr.sum for 3 ## levels)
mat <- contr.sum(3)
## You can add the names you want to see in the output
## Be carefull that you give the correct names to the concerned
## column. Otherwise there is the big danger of misinterpretation.
colnames(mat) <- c(": A against rest", ": B against rest") ## Attatch the contrast at your factor "group" dat[,"group"] <- C(dat[,"group"],mat)
## Now calculate the lme
library(nlme)
reg.lme <- lme(area ~ group, data = dat, random = ~ 1|species) summary(reg.lme)

Maybe someone has a better idea how to do it generally.

Hope this helps

Christoph Buser



Christoph Buser <buser@stat.math.ethz.ch> Seminar fuer Statistik, LEO C13
ETH (Federal Inst. Technology)	8092 Zurich	 SWITZERLAND
phone: x-41-44-632-4673		fax: 632-1228

http://stat.ethz.ch/~buser/

Ghislain Vieilledent writes:
> Good morning,
>
> I used in R contr.sum for the contrast in a lme model:
>
> > options(contrasts=c("contr.sum","contr.poly"))
> > Septo5.lme<-lme(Septo~Variete+DateSemi,Data4.Iso,random=~1|LieuDit)
> > intervals(Septo5.lme)$fixed
> lower est. upper
> (Intercept) 17.0644033 23.106110 29.147816
> Variete1 9.5819873 17.335324 25.088661
> Variete2 -3.3794907 6.816101 17.011692
> Variete3 -0.5636915 8.452890 17.469472
> Variete4 -22.8923812 -10.914912 1.062558
> Variete5 -10.7152821 -1.865884 6.983515
> Variete6 0.2743390 9.492175 18.710012
> Variete7 -23.7943250 -15.070737 -6.347148
> Variete8 -21.7310554 -12.380475 -3.029895
> Variete9 -27.9782575 -17.480555 -6.982852
> DateSemi1 -5.7903419 -1.547875 2.694592
> DateSemi2 3.6571596 8.428417 13.199675
> attr(,"label")
> [1] "Fixed effects:"
>
> How is it possible to obtain a return with the name of my factor's levels as
> with contr.treatment ?
>
> Thanks for you help.
>
> --
> Ghislain Vieilledent
> 30, rue Bernard Ortet 31 500 TOULOUSE
> 06 24 62 65 07
>
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>
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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.html Received on Thu Jul 14 01:45:38 2005

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