[R] rpart with interval censored data crashes R

[David Winsemius]

On a Leopard Mac with the Urbanek compiled 64 bit R, one sees this:

 > library(rpart)
 > library(survival)
Loading required package: splines
 > fit<-rpart(Surv(N,Y,type="interval2")~Salt+pH+Temp, data=myD)

  *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
  1: .C(C_rpartexp2, as.integer(length(dtimes)),  
as.double(dtimes),     as.double(.Machine$double.eps), keep =  
integer(length(dtimes)))
  2: (get(paste("rpart", method, sep = ".")))(Y, offset, , wt)
  3: rpart(Surv(N, Y, type = "interval2") ~ Salt + pH + Temp, data =  
myD)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

Choosing "4" does save the workspace.
-- 
David Winsemius

On Jan 9, 2009, at 9:04 AM, Keith Jewell wrote:

> Hi Everyone,
>
> This example code results in R 'crashing'; that is the R application  
> closes
> with no warnings or error messages.
> #-----------------------
> myD <- read.table(stdin(), header=TRUE, nrows=20)
> Broth Salt   pH Temp    N  Y Growth
> 1        310    9.0 2.92      10 90.0 NA            0
> 2        615    6.0 7.82      30  1.0  2            1
> 3        217    2.0 7.34      10  7.0  8            1
> 4        338   10.0 4.44      10 90.0 NA            0
> 5        240    4.0 7.33      10 20.0 21            1
> 6        336   10.0 3.90      10 90.0 NA            0
> 7        279    7.0 6.73      10 90.0 NA            0
> 8       1021    9.0 5.03      45  8.0  9            1
> 9        974    7.0 4.01      45 90.0 NA            0
> 10       265    7.0 2.93      10 90.0 NA            0
> 11       934    4.0 5.28      45  0.1  1            1
> 12       669    9.0 5.03      30 90.0 NA            0
> 13       875   10.0 6.24      37  1.0  2            1
> 14       385    2.0 5.84      20  1.0  2            1
> 15       562    2.0 5.84      30  0.1  1            1
> 16       718    0.5 5.54      37  0.1  1            1
> 17       845    9.0 5.03      37  3.0  6            1
> 18       913    2.0 5.84      45  0.1  1            1
> 19       577    4.0 4.10      30 90.0 NA            0
> 20        20    0.5 7.44       8 24.0 27            1
>
> library(rpart)
> library(survival)
> fit<-rpart(Surv(N,Y,type="interval2")~Salt+pH+Temp, data=myD)
> #---------------------
>
> Professor Ripley helpfully pointed out that the documentation does  
> not say
> that interval censoring is supported, and indeed this seems only to  
> happen
> with interval censored data.
>
> ?rpart indicates that the dependent variable may be a survival object.
> Neither ?rpart nor "An Introduction to Recursive Partitioning Using  
> the
> RPART Routines" (Therneau et al 1997) suggest that the dependent  
> variable
> may contain interval censored data, but neither do they suggest it
> shouldn't; i.e. as far as I'm aware (!) this restriction is not  
> documented.
>
> This post has three purposes:
>
> 1) Bring this behaviour - especially the crash in response to 'bad'  
> data -
> to the attention of the authors.
>
> 2) Seek an explanation of the restriction (if intentional). In my
> simplicity, it seems that interval censored data should be easier to  
> handle
> than left or right censored - after all the information content is  
> greater.
>
> 3) Seek guidance on how to work around the problem. I'm minded to  
> replace
> the interval censored data by the mid points of the intervals. Does  
> anyone
> have any comments on such an approach?
>
> Any comments gratefully received.
>
> Keith Jewell
> ==========================================
> Version:
> platform = i386-pc-mingw32
> arch = i386
> os = mingw32
> system = i386, mingw32
> status = Patched
> major = 2
> minor = 8.1
> year = 2009
> month = 01
> day = 07
> svn rev = 47502
> language = R
> version.string = R version 2.8.1 Patched (2009-01-07 r47502)
>
> Windows Server 2003 x64 (build 3790) Service Pack 2
>
> Locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> Search Path:
> .GlobalEnv, package:stats, package:graphics, package:grDevices,
> package:utils, package:datasets, package:methods, Autoloads,  
> package:base
>
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