R help - Apr 2009 - Function call error in cph/survest (package Design)

Dear UseR,

I do not know if this a problem with me, my data or cph/survest in package
design. The example below works with a standard data set, but not with my
data, but I cannot locate the problem.

Note that I am using an older package of survival to avoid a problem with
the newly renamed function in survival meeting Design. 

Dieter

# First, check standard example to make sure
library(Design)
data(ovarian)
dd = datadist(ovarian)
options(datadist="dd")
ovarian$rx = as.factor(ovarian$rx)
cp = cph(Surv(futime,fustat)~rx,data=ovarian,surv=TRUE,x=TRUE,y=TRUE)
summary(cp)
# works ok
survest(cp,levels(ovarian$rx),times=500)

# Small data set, 223 rows, 3650 bytes
cc = read.table("http://www.menne-biomed.de/uni/cc.csv",header=TRUE)
#cc = read.table("cc.csv",header=TRUE)
dd = datadist(cc)
cp = cph(Surv(DaysToEvent,event)~ITTGroup,data=cc,surv=TRUE,x=TRUE,y=TRUE)

survest(cp,levels(cc$ITTGroup),times=100)

#Error in survfit.cph(list(coefficients = c(0.435291247251185,
-0.143015493753166 :
#  NA/NaN/Inf in foreign function call (arg 13)
#In addition: Warning message:
#NAs introduced by coercion

#-------------------

summary(cc)

  DaysToEvent      event         ITTGroup
 Min.   :  3.0   Mode :logical   Anti:76
 1st Qu.: 22.0   FALSE:89        Con :76
 Median : 70.0   TRUE :134       Pla :71
 Mean   :108.3   NA's :0
 3rd Qu.:224.0
 Max.   :261.0


#--------------------------------
 > sessionInfo()
R version 2.9.0 Under development (unstable) (2009-03-13 r48127)
i386-pc-mingw32

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=Germ
an_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

attached base packages:
[1] splines   stats     graphics  grDevices datasets  utils     methods
base

other attached packages: (Note: older version of survival to avoid problems
with Design)
[1] Design_2.1-2  survival_2.34 Hmisc_3.5-2

loaded via a namespace (and not attached):
[1] cluster_1.11.12 grid_2.9.0      lattice_0.17-20
tools_2.9.0
>

Dieter Menne wrote:
> 
> I do not know if this a problem with me, my data or cph/survest in package
> design. The example below works with a standard data set, but not with my
> data, but I cannot locate the problem.
> 
Dieter Menne found out after hours, that in one case and explicit cast is
required, but none in the other, and has no idea why.

#---------------------------------------
library(Design)
data(ovarian)
dd = datadist(ovarian)
options(datadist="dd")
ovarian$rx = as.factor(ovarian$rx)
cp = cph(Surv(futime,fustat)~rx,data=ovarian,surv=TRUE,x=TRUE,y=TRUE)
summary(cp)
survplot(cp,rx=NA)
# works ok, without casting to a data frame
survest(cp,newdata=levels(ovarian$rx),what="survival",times=500)

# Small data set, 223 rows, 3650 bytes
cc = read.table("http://www.menne-biomed.de/uni/cc.csv",header=TRUE)
#cc = read.table("cc.csv",header=TRUE)
dd = datadist(cc)
cp = cph(Surv(DaysToEvent,event)~ITTGroup,data=cc,surv=TRUE,x=TRUE,y=TRUE)
survplot(cp,ITTGroup=NA)
summary(cp)

survest(cp,newdata=levels(cc$ITTGroup),times=200)
#Error in survfit.cph(list(coefficients = c(0.435291247251185,
-0.143015493753166 :
#  NA/NaN/Inf in foreign function call (arg 13)
#In addition: Warning message:
#NAs introduced by coercion

# Works when explicitly converted to a data frame
survest(cp,newdata=data.frame(ITTGroup=levels(cc$ITTGroup)),times=200)

 

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