R help - May 2005 - body of non-visible function

Hello,
Is there any possibility in R to see the body of the non-visible 
function, for
example princomp?
If I do :

 > methods(princomp)

so, I get that princomp.default and princomp.formula are non-visible 
functions and
body(princomp.default) doesnt show it.

In particular, I guess I have a very nave question
Id like to see how scores calculation is implemented in the function
princomp. Because when I multiply my data matrix on the matrix of loadings
 >data.matrix %*% princomp(data.matrix, scores=T)$loadings

I get different result than just doing

 >princomp(data.matrix, scores=T)$scores.

Thanks.
Anna

> From: Anna Oganyan
> 
> Hello,
> Is there any possibility in R to see the body of the
"non-visible"
> function, for
> example "princomp"?
> If I do :
> 
>  > methods(princomp)
> 
> so, I get that princomp.default and princomp.formula are non-visible 
> functions and
> body(princomp.default) doesn't show it.
You may want to learn about getAnywhere() and getS3method().

 
> In particular, I guess I have a very na??ve question...
> I'd like to see how scores calculation is implemented in the function
> princomp. Because when I multiply my data matrix on the 
> matrix of loadings
>  >data.matrix %*% princomp(data.matrix, scores=T)$loadings
> 
> I get different result than just doing
> 
>  >princomp(data.matrix, scores=T)$scores.
Variables are centered and scaled, so you want to do

  scale(data.matrix) %*% loadings(princomp(data.matrix))

Andy

 
> Thanks.
> Anna
> 
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> 
> 
>

getS3method("princomp", "default").
getAnywhere("princomp.default")

The first of these is in the See Also of ?methods.

On Thu, 5 May 2005, Anna Oganyan wrote:
> Hello,
> Is there any possibility in R to see the body of the 
non-visible
 
> function, for
> example 
princomp
?
> If I do :
>
>> methods(princomp)
>
> so, I get that princomp.default and princomp.formula are non-visible 
> functions and
> body(princomp.default) doesnt show it.
>
> In particular, I guess I have a very na?ve question&
> Id like to see how scores calculation is implemented in the function
> princomp. Because when I multiply my data matrix on the matrix of loadings
>> data.matrix %*% princomp(data.matrix, scores=T)$loadings
>
> I get different result than just doing
>
>> princomp(data.matrix, scores=T)$scores.
You have forgotten to centre your data.  It may be more helpful to look at 
the predict method.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Anna Oganyan wrote on 5/5/2005 7:42 AM:
> Hello,
> Is there any possibility in R to see the body of the non-visible 
> function, for
> example princomp?
> If I do :
> 
>  > methods(princomp)
> 
> so, I get that princomp.default and princomp.formula are non-visible 
> functions and
> body(princomp.default) doesnt show it.
> 
> In particular, I guess I have a very nave question
> Id like to see how scores calculation is implemented in the function
> princomp. Because when I multiply my data matrix on the matrix of loadings
>  >data.matrix %*% princomp(data.matrix, scores=T)$loadings
> 
> I get different result than just doing
> 
>  >princomp(data.matrix, scores=T)$scores.
> 
> Thanks.
> Anna
> 

Hi Anna,

Use getAnywhere("princomp.default") or stats:::princomp.default. This 
has to do with princomp.default not being exported in the stats package 
NAMESPACE.

As for the difference, the scores are based on centering the columns of 
data.matrix before determining the principal components. For example:

 > X <- as.matrix(USArrests)
 > Xc <- sweep(X, 2, colMeans(X), "-")
 > pc <- princomp(X, scores = TRUE) # inappropriate, see ?princomp
 > str(pc$scores)
  num [1:50, 1:4]  -64.8  -92.8 -124.1  -18.3 -107.4 ...
  - attr(*, "dimnames")=List of 2
   ..$ : chr [1:50] "Alabama" "Alaska" "Arizona"
"Arkansas" ...
   ..$ : chr [1:4] "Comp.1" "Comp.2" "Comp.3"
"Comp.4"
 > Xl <- Xc %*% loadings(pc)
 > str(Xl)
  num [1:50, 1:4]  -64.8  -92.8 -124.1  -18.3 -107.4 ...
  - attr(*, "dimnames")=List of 2
   ..$ : chr [1:50] "Alabama" "Alaska" "Arizona"
"Arkansas" ...
   ..$ : chr [1:4] "Comp.1" "Comp.2" "Comp.3"
"Comp.4"
 > sum(abs(Xl - pc$scores))
[1] 4.97999e-12
 >

Finally, "data.matrix" is a function in the base package. I would
avoid
using it as a variable name.

--sundar