[R] Design matrix question
Steven McKinney
smckinney at bccrc.ca
Thu May 17 04:34:19 CEST 2007
Hi useRs,
Perhaps I am having a senior moment?
I have a nested variable situation to model,
toy example:
> df <- data.frame(A = factor(c("a", "a", "x", "x"), levels = c("x", "a")),
+ B = factor(c("b", "x", "x", "x"), levels = c("x", "b")))
>
> df
A B
1 a b
2 a x
3 x x
4 x x
So of course the full design matrix is singular
> model.matrix(~ A * B, df)
(Intercept) Aa Bb Aa:Bb
1 1 1 1 1
2 1 1 0 0
3 1 0 0 0
4 1 0 0 0
attr(,"assign")
[1] 0 1 2 3
attr(,"contrasts")
attr(,"contrasts")$A
[1] "contr.treatment"
attr(,"contrasts")$B
[1] "contr.treatment"
I'd like not to have the B term main effect in the model
> model.matrix(~ A * B - B, df)
(Intercept) Aa Ax:Bb Aa:Bb
1 1 1 0 1
2 1 1 0 0
3 1 0 0 0
4 1 0 0 0
attr(,"assign")
[1] 0 1 2 2
attr(,"contrasts")
attr(,"contrasts")$A
[1] "contr.treatment"
attr(,"contrasts")$B
[1] "contr.treatment"
>
How do I get model.matrix to not add that
column of zeroes?
Why does model.matrix add that column of zeroes?
Is this a bug, or a senior moment?
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney at bccrc.ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
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