R devel - Dec 2012 - as.matrix.Surv -- R core question/opinions

1. A Surv object is a matrix with some extra attributes.  The as.matrix.Surv
function
removes the extras but otherwise leaves it as is.

2. The last several versions of the survival library were accidentally missing
the
S3method('as.matrix', 'Surv') line from their NAMESPACE file. 
(Instead it's position is
held by a duplicate of the line just above it in the NAMESPACE file, suggesting
a
copy/paste error).  As a consequence the as.matrix.Surv function was effectively
ignored,
and the default method was being used.
    The as.matrix.default function leaves anything with a "dim"
attribute alone.

3. In my current about-to-submit-to-CRAN  version of survival the missing
NAMESPACE line
was restored.  This breaks one function in one package (rms) which calls
"as.matrix(y)" on
a Surv object but then later looks at the "type" attribute of y.

  So now to the design question: should the as.matrix.Surv function
"sanitize" the result
by removing the extra attributes, or should it leave them alone?  The first
seems cleaner;
my accidental multi-year test of leaving them in, however, clearly shows that it
does no
harm.

Terry T.

I agree that it's cleaner to remove the extra attributes -- that's the
point of as.matrix.Surv(), to produce a matrix that doesn't include any
extra details of how Surv objects are implemented.

   -thomas


On Fri, Dec 7, 2012 at 3:48 AM, Terry Therneau <therneau@mayo.edu> wrote:
> 1. A Surv object is a matrix with some extra attributes.  The
> as.matrix.Surv function removes the extras but otherwise leaves it as is.
>
> 2. The last several versions of the survival library were accidentally
> missing the S3method('as.matrix', 'Surv') line from their
NAMESPACE file.
>  (Instead it's position is held by a duplicate of the line just above
it in
> the NAMESPACE file, suggesting a copy/paste error).  As a consequence the
> as.matrix.Surv function was effectively ignored, and the default method was
> being used.
>    The as.matrix.default function leaves anything with a "dim"
attribute
> alone.
>
> 3. In my current about-to-submit-to-CRAN  version of survival the missing
> NAMESPACE line was restored.  This breaks one function in one package (rms)
> which calls "as.matrix(y)" on a Surv object but then later looks
at the
> "type" attribute of y.
>
>  So now to the design question: should the as.matrix.Surv function
> "sanitize" the result by removing the extra attributes, or should
it leave
> them alone?  The first seems cleaner; my accidental multi-year test of
> leaving them in, however, clearly shows that it does no harm.
>
> Terry T.
>
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>


-- 
Thomas Lumley
Professor of Biostatistics
University of Auckland

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