From ggrothendieck at gmail.com  Wed Apr 21 20:00:33 2010
From: ggrothendieck at gmail.com (Gabor Grothendieck)
Date: Wed, 21 Apr 2010 14:00:33 -0400
Subject: [Rd] Bugs? when dealing with contrasts
Message-ID: <l2u971536df1004211100q9beecbep1bceb5bbbd3b8175@mail.gmail.com>

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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"



[Rd] Bugs? when dealing with contrasts
Gabor Grothendieck