On 11/30/2012 4:53 AM, Terry Therneau wrote:
I'm puzzled by as.matrix. It appears to work differently for Surv objects.
Here is a session from my computer:
tmt% R --vanilla
> library(survival)
Loading required package: splines
> ytest <- Surv(1:3, c(1,0,1))
> is.matrix(ytest)
>[1] TRUE
It seems that survival:::as.matrix.Surv is not recognized as a
dispatch-able method for as.matrix:
> methods("as.matrix")
[1] as.matrix.data.frame as.matrix.default as.matrix.dist*
[4] as.matrix.noquote as.matrix.POSIXlt as.matrix.raster*
[7] as.matrix.ratetable*
I'm guessing it is not declared as such in the NAMESPACE file.
> attr(ytest, 'type')
[1] "right"
> attr(as.matrix(ytest), 'type')
[1] "right"
>
> y2 <- ytest
> class(y2) <- "charlie"
> as.matrix.charlie <- survival:::as.matrix.Surv
This new function does show up:
> methods("as.matrix")
[1] as.matrix.charlie as.matrix.data.frame as.matrix.default
[4] as.matrix.dist* as.matrix.noquote as.matrix.POSIXlt
[7] as.matrix.raster* as.matrix.ratetable*
and is being called as expected.
> attr(y2, 'type')
[1] "right"
> attr(as.matrix(y2), 'type')
NULL
> survival:::as.matrix.Surv
function (x)
{
y <- unclass(x)
attr(y, "type") <- NULL
y
}
<bytecode: 0x91c1610>
<environment: namespace:survival>
What is being called by as.matrix(ytest) is as.matrix.default
> as.matrix.default
function (x, ...)
{
if (is.matrix(x))
x
else array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x), NULL)
else NULL)
}
<bytecode: 0x000000000631a0b8>
<environment: namespace:base>
which will just return ytest is is.matrix(ytest) is TRUE (as you show).
--------
It appears that Surv objects are being processed by as.matrix.default,
but "charlie" objects by the
actual method. One more verification:
> attr(survival:::as.matrix.Surv(ytest), 'type')
NULL
> attr(as.matrix.default(y2), 'type')
[1] "right"
Correct.
Context: In testing the next survival release (2.37), it has lost this
"special" behavior. One package that depends on survival expects this
behavior and thus fails. I'm at a loss to figure out how my package got
this attribute in the first place, or how it lost it. Can anyone shed
light?
The behavior I showed above was with 2.36-14, even.
In your NAMESPACE file, there are two lines that say
S3method(as.matrix, ratetable)
I bet one of them was meant to be
S3method(as.matrix, Surv)
Terry Therneau
PS I'm on vacation for the next few days so will be intermittent with
email. (Off to see my first grandchild!)
---------------------
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] survival_2.36-14
--
Brian S. Diggs, PhD
Senior Research Associate, Department of Surgery
Oregon Health & Science University
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