From therneau at mayo.edu  Fri Nov 30 13:53:36 2012
From: therneau at mayo.edu (Terry Therneau)
Date: Fri, 30 Nov 2012 06:53:36 -0600
Subject: [Rd] Baffled with as.matrix
Message-ID: <50B8AC50.3010903@mayo.edu>

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

 > attr(ytest, 'type')
[1] "right"
 > attr(as.matrix(ytest), 'type')
[1] "right"
 >
 > y2 <- ytest
 > class(y2) <- "charlie"
 > as.matrix.charlie <- survival:::as.matrix.Surv
 > 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>

--------
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"

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?

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



[Rd] Baffled with as.matrix
Terry Therneau