[R] survexp - example produces error

[Heinz Tuechler]

Follow up:

The critical line seems to be in survexp around line 97

rdata <- data.frame(eval(rcall, m))

If changed to:

old.stringsAsFactors <- options()$stringsAsFactors
options(stringsAsFactors=TRUE)
rdata <- data.frame(eval(rcall, m))  ### <- seems to be critical
options(stringsAsFactors=old.stringsAsFactors)

it seems to work.

Heinz

At 31.12.2010 15:53 +0100, Heinz Tuechler wrote:
>Dear Peter, Dear All,
>
>a further attempt led me to an answer. If I set 
>options(stringsAsFactors=TRUE), which I usually have set to FALSE, 
>no error occurs.
>I am, however not happy with this solution.
>
>Heinz
>
>Thank you, Peter
>
>after setting options(error=recover), see the output below, once for 
>frame number 2, which I suspect to be the problem, once for frame number 1.
>
>Heinz
>
> > expect <-
>+   survexp(futime ~ ratetable(age=(accept.dt - birth.dt),
>+                              sex=1,year=accept.dt,race="white"),
>+           jasa, cohort=FALSE,
>+           ratetable=survexp.usr)
>Error in floor(temp) : Non-numeric argument to mathematical function
>
>Enter a frame number, or 0 to exit
>
>1: survexp(futime ~ ratetable(age = (accept.dt - birth.dt), sex = 1, year = ac
>2: match.ratetable(rdata, ratetable)
>
>Selection: 2
>Called from: top level
>Browse[1]> temp
>   [1] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [10] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [19] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [28] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [37] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [46] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [55] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [64] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [73] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [82] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>  [91] "white" "white" "white" "white" "white" "white" "white" "white" "white"
>[100] "white" "white" "white" "white"
>Browse[1]> Q
> >
>
>There is also 'temp' in frame number 1.
>
> > expect <-
>+   survexp(futime ~ ratetable(age=(accept.dt - birth.dt),
>+                              sex=1,year=accept.dt,race="white"),
>+           jasa, cohort=FALSE,
>+           ratetable=survexp.usr)
>Error in floor(temp) : Non-numeric argument to mathematical function
>
>Enter a frame number, or 0 to exit
>
>1: survexp(futime ~ ratetable(age = (accept.dt - birth.dt), sex = 1, year = ac
>2: match.ratetable(rdata, ratetable)
>
>Selection: 1
>Called from: top level
>Browse[1]> temp
>  [1]   49    5   15   38   17    2  674   39   84   57  152    7 
> 80 1386    0
>[16]  307   35   42   36   27 1031   50  732  218 1799 
>1400  262   71   34  851
>[31]   76 1586 1571   11   99   65    4   52 1407 
>1321    1   44  995    8 1141
>[46]  979  284  101  187   60  941  148  342  915   67   68  841 
>583   77   31
>[61]  669   29  619  595   89   16  544   20  514   95  481  444 
>427   79  333
>[76]  396  109  369  206  185  339  264  164  179  130  108   30   10
>Browse[1]> Q
>
>
>
>At 31.12.2010 13:46 +0100, peter dalgaard wrote:
>
>>On Dec 31, 2010, at 10:21 , Heinz Tuechler wrote:
>>
>> > Dear All,
>> >
>> > reposting, because I did not find a solution, maybe someone 
>> could check the example below.
>> >
>> > It's taken from the help page of survdiff. Executing it, gives the error
>> >
>> > "Error in floor(temp) : Non-numeric argument to mathematical function"
>>
>>Hmm, it's not happening to me (Mac OSX) either with 2.12.1 or the 
>>current R-patched (r53892). Could be a platform issue (sounds 
>>unlikely), a local user issue, or a locale one.
>>
>>Could you set options(error=recover) and find out what is the value 
>>of "temp" when the error occurs?
>>
>> >
>> > best regards,
>> >
>> > Heinz
>> >
>> > library(survival)
>> >
>> > ## Example from help page of survdiff
>> > ## Expected survival for heart transplant patients based on
>> > ## US mortality tables
>> > expect <-
>> >  survexp(futime ~ ratetable(age=(accept.dt - birth.dt),
>> >                             sex=1,year=accept.dt,race="white"),
>> >          jasa, cohort=FALSE,
>> >          ratetable=survexp.usr)
>> >
>> > Error in floor(temp) : Non-numeric argument to mathematical function
>> >
>> > sessionInfo('survival')
>> >
>> > R version 2.12.1 Patched (2010-12-18 r53869)
>> > Platform: i386-pc-mingw32/i386 (32-bit)
>> >
>> > locale:
>> > [1] LC_COLLATE=German_Switzerland.1252  LC_CTYPE=German_Switzerland.1252
>> > [3] LC_MONETARY=German_Switzerland.1252 LC_NUMERIC=C
>> > [5] LC_TIME=German_Switzerland.1252
>> >
>> > attached base packages:
>> > character(0)
>> >
>> > other attached packages:
>> > [1] survival_2.36-2
>> >
>> > loaded via a namespace (and not attached):
>> > [1] base_2.12.1      graphics_2.12.1  grDevices_2.12.1 methods_2.12.1
>> > [5] splines_2.12.1   stats_2.12.1     tools_2.12.1     utils_2.12.1
>> > > traceback()
>> > 2: match.ratetable(rdata, ratetable)
>> > 1: survexp(futime ~ ratetable(age = (accept.dt - birth.dt), sex = 1,
>> >       year = accept.dt, race = "white"), jasa, cohort = FALSE,
>> >       ratetable = survexp.usr)
>> > >
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>>--
>>Peter Dalgaard
>>Center for Statistics, Copenhagen Business School
>>Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>Phone: (+45)38153501
>>Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com