[R] Help in using PCR

[Gavin Simpson]

On Wed, 2008-07-02 at 10:32 +0200, Bjørn-Helge Mevik wrote:
> Gavin Simpson <gavin.simpson at ucl.ac.uk> writes:
> 
> > Ok, lets sort this out. [Not tested as I don't have your data]
> >
> > df <- data.frame(resp = cancerv1[, 408], 
> >                  VARS = as.matrix(cancerv1[, 2:407])
> 
> Actually, you _do_ need an I() here:
> 
> df <- data.frame(resp = cancerv1[, 408], 
>                  VARS = I(as.matrix(cancerv1[, 2:407])))
> 
> otherwise data.frame() will split the matrix into single coloumn variables.

Doh! Thanks for pointing that out! I knew I'd get something seriously
wrong there when I added the immortal words "Not tested...". That'll
teach me to take shortcuts and not use dummy or inbuilt data as an
example.

This raises another issue:

> dat <- data.frame(matrix(rnorm(101 * 20), ncol = 101, nrow = 20))
> df <- data.frame(resp = dat[,1], VARS = I(as.matrix(dat[, 2:101])))
> str(df)
'data.frame':   20 obs. of  2 variables:
 $ resp: num   0.149 -0.715  0.069  0.560 -0.321 ...
 $ VARS: AsIs [1:20, 1:100] 0.602859.... 0.517785.... -1.02003....
-2.70378.... -0.95322.... ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr  "X2" "X3" "X4" "X5" ...
> class(df$VARS)
[1] "AsIs"

The class is AsIs for $VARS. But if I look at your yarn data set for
example, the NIR component is of class "matrix":

> str(yarn)
'data.frame':   28 obs. of  3 variables:
 $ NIR    : num [1:28, 1:268] 3.07 3.07 3.08 3.08 3.10 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : NULL
 $ density: num  100.0  80.2  79.5  60.8  60.0 ...
 $ train  : logi  TRUE TRUE TRUE TRUE TRUE TRUE ...
> class(yarn$NIR)
[1] "matrix"

How did you achieve this?

Cheers

G

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