R version 2.10.1 (2009-12-14)
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Below are two cases where I don't seem to be getting contr.sum
contrasts even though they were specified. Are these bugs?
The first case is an interaction between continuous and factor variables.
The second case contrasts= was specified as an arg to lm. The second
works ok if we set the contrasts through options but not if we set it
through an lm argument.
>
> # 1. In this case I don't seem to be getting contr.sum contrasts:
>
> options(contrasts = c("contr.sum", "contr.poly"))
> getOption("contrasts")
[1] "contr.sum" "contr.poly"
> scores <- rep(seq(-2, 2), 3); scores
[1] -2 -1 0 1 2 -2 -1 0 1 2 -2 -1 0 1 2
> fac <- gl(3, 5); fac
[1] 1 1 1 1 1 2 2 2 2 2 3 3 3 3 3
Levels: 1 2 3
>
> # I get this:
> model.matrix(~ scores:fac)
(Intercept) scores:fac1 scores:fac2 scores:fac3
1 1 -2 0 0
2 1 -1 0 0
3 1 0 0 0
4 1 1 0 0
5 1 2 0 0
6 1 0 -2 0
7 1 0 -1 0
8 1 0 0 0
9 1 0 1 0
10 1 0 2 0
11 1 0 0 -2
12 1 0 0 -1
13 1 0 0 0
14 1 0 0 1
15 1 0 0 2
attr(,"assign")
[1] 0 1 1 1
attr(,"contrasts")
attr(,"contrasts")$fac
[1] "contr.sum"
>
> # But I was expecting this since I am using contr.sum
> cbind(1, model.matrix(~ fac)[,2:3] * scores)
fac1 fac2
1 1 -2 0
2 1 -1 0
3 1 0 0
4 1 1 0
5 1 2 0
6 1 0 -2
7 1 0 -1
8 1 0 0
9 1 0 1
10 1 0 2
11 1 2 2
12 1 1 1
13 1 0 0
14 1 -1 -1
15 1 -2 -2
>
>
> # 2.
> # here I don't get contr.sum but rather get contr.treatment
> options(contrasts = c("contr.treatment", "contr.poly"))
> getOption("contrasts")
[1] "contr.treatment" "contr.poly"
> model.matrix(lm(seq(15) ~ fac, contrasts = c("contr.sum", "contr.poly")))
(Intercept) fac2 fac3
1 1 0 0
2 1 0 0
3 1 0 0
4 1 0 0
5 1 0 0
6 1 1 0
7 1 1 0
8 1 1 0
9 1 1 0
10 1 1 0
11 1 0 1
12 1 0 1
13 1 0 1
14 1 0 1
15 1 0 1
attr(,"assign")
[1] 0 1 1
attr(,"contrasts")
attr(,"contrasts")$fac
[1] "contr.treatment"
> model.matrix(lm(seq(15) ~ fac)) # same
(Intercept) fac2 fac3
1 1 0 0
2 1 0 0
3 1 0 0
4 1 0 0
5 1 0 0
6 1 1 0
7 1 1 0
8 1 1 0
9 1 1 0
10 1 1 0
11 1 0 1
12 1 0 1
13 1 0 1
14 1 0 1
15 1 0 1
attr(,"assign")
[1] 0 1 1
attr(,"contrasts")
attr(,"contrasts")$fac
[1] "contr.treatment"
>
> # I was expecting the first one to give me this
> options(contrasts = c("contr.sum", "contr.poly"))
> model.matrix(lm(seq(15) ~ fac))
(Intercept) fac1 fac2
1 1 1 0
2 1 1 0
3 1 1 0
4 1 1 0
5 1 1 0
6 1 0 1
7 1 0 1
8 1 0 1
9 1 0 1
10 1 0 1
11 1 -1 -1
12 1 -1 -1
13 1 -1 -1
14 1 -1 -1
15 1 -1 -1
attr(,"assign")
[1] 0 1 1
attr(,"contrasts")
attr(,"contrasts")$fac
[1] "contr.sum"
>
> R.version.string
[1] "R version 2.10.1 (2009-12-14)"
> win.version()
[1] "Windows Vista (build 6002) Service Pack 2"
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