[R] Contrasts in Penalized Package

[Bill.Venables at csiro.au]

The key line is

    prep <- .checkinput(match.call(), parent.frame())
 
Among other things the model matrix is built in .checkinput( ) which is not exported from the package namespace.  So you have to get rough with it and use

penalized:::.checkinput

and then you see these line of code

        options(contrasts = c(unordered = "contr.none", ordered = "contr.diff"))

and the scene is set.  The selection of contrasts is hardwired and to get around it you would need to hack the package, not a great idea.  
The namespace will get you if you try to mask contr.none with a function of your own, for example.

Bill Venables.


________________________________________
From: r-help-bounces at r-project.org [r-help-bounces at r-project.org] On Behalf Of Lars Bishop [lars52r at gmail.com]
Sent: 20 May 2011 20:52
To: r-help at r-project.org
Subject: [R] Contrasts in Penalized Package

Hi,

The "penalized" documentation says that "Unordered factors are turned
into as many dummy variables as the factor has levels". This is done
by a function in the package called contr.none. I'm trying to figure
out how exactly is a model matrix created with this contrast option
when the user calls the function with a formula. I typed
"library(penalized) ; penalized" but couldn't point the part of the
code where this is done.

I'll appreciate any help on this.

Lars.

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