Hi there,
I have a rather large data set and perform the following cox model:
test1 <- list(tstart,tstop,death1,chemo1,radio1,horm1)
out1<-coxph( Surv(tstart,tstop, death1) ~
chemo1+chemo1:log(tstop+1)+horm1+horm1:log(tstop+1)+age1+grade1+grade1:log(tstop+1)+positive1+positive1:log(tstop+1)+size1+size1:log(tstop+1),
test1)
out1
Up to here everything works fine (with each covariate having a length of 289205)
Now I want to see a specific profile of the above model so I ask for:
x11()
profilbig2=(survfit(out1,newdata=data.frame(chemo1=rep(0,length(chemo1)),horm1=rep(0,length(chemo1)),age1=rep(mean(age1),length(chemo1)),grade1=rep(0,length(chemo1)),positive1=rep(1,length(chemo1)),size1=rep(mean(size1),length(chemo1))
)))
plot(profilbig2,col="blue")
and I get the following error:
Error: cannot allocate vector of size 1.5 Gb
In addition: Warning messages:
1: In vector("double", length) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In vector("double", length) :
Reached total allocation of 1535Mb: see help(memory.size)
3: In vector("double", length) :
Reached total allocation of 1535Mb: see help(memory.size)
4: In vector("double", length) :
Reached total allocation of 1535Mb: see help(memory.size)
I am wondering why is that happening since I manage to fit the model. Shouldn't
the memory problem pop up earlier when I was fitting the model? So now I fit
the model but still cannot study a ceratin profile?? Can anyone suggest
something? I am not an advanced user of R, do I type something wrong or can I
do something more clever to see a profile of a hypothetical subject?
Thanx in advance for any answers..
(2 GB RAM).
P.S. I noticed in the help the "--max-mem-size" but I am not quite sure how to
use it..
Leo.
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