2008/2/27, Lore Merdrignac <[EMAIL PROTECTED]>:
>
> Thanks for answering.
> I had already tested to split the expression but there is still a problem
> with the function survfit(). Nevertheless this expression works with R, but
> I have to implement it with python. Indeed, I am trying to create a software
> for survival analysis using python language...
>
> >>> s=r.Surv(t,d)
> >>> ss=r.survfit(s)
> Traceback (most recent call last):
> File "<interactive input>", line 1, in ?
> RPy_RException: Erreur dans parse(text = paste(deparse(call[[2]]), 1, sep =
> "~")) :
> unexpected numeric constant dans :
> "structure(c(6L, 6L, 6L, 6L, 6L, 9L, 9L, 9L, 12L, 12L, 12L, 12L, ~1
> 12L"
>
> and obviously, I get then :
>
> >>> survPlot = r.get("plot.survfit", envir=r.getNamespace("survival"))
> >>> survPlot(sf)
> Traceback (most recent call last):
> File "<interactive input>", line 1, in ?
> NameError: name 'sf' is not defined
Wouldn't it be because the variable name 'sf' is indeed not defined ?
(in your version above, the variable name is 'ss').
Anyway, because of the error that variable will obviously not be created
(and I was shooting in the dark, thinking that the error was coming from
the call to "plot"... now we know that it is coming from "survfit").
Out of curiosity, what is saying "print(s)" ?
> Lore.
>
> ________________________________
> > Date: Wed, 27 Feb 2008 11:48:12 +0100
> > From: [EMAIL PROTECTED]
> > To: rpy-list@lists.sourceforge.net
> > Subject: Re: [Rpy] package : survival
>
> >
> > 2008/2/27, Lore Merdrignac <[EMAIL PROTECTED]>:
> > >
> > > Hi,
> > > I have already posted a first problem of "NO_CONVERSION" with the
> package
> > > SURVIVAL. But I still have a problem by using the function survfit() of
> the
> > > package.
> > > Here is the code :
> > >
> > > >>> from rpy import *
> > > >>> r.library("survival")
> > > >>> set_default_mode(NO_CONVERSION)
> > > >>> d=r.rep(1,41)
> > > >>> t=r.c( r.rep(6,5), r.rep(9,3) , r.rep(12,24), r.rep(15,9) )
> > > >>> r.plot(r.survfit(r.Surv(t,d)))
> > > Traceback (most recent call last):
> > > File "<interactive input>", line 1, in ?
> > > RPy_RException: Erreur dans parse(text = paste(deparse(call[[2]]), 1,
> sep =
> > > "~")) :
> > > unexpected numeric constant dans :
> > > "structure(c(6L, 6L, 6L, 6L, 6L, 9L, 9L, 9L, 12L, 12L, 12L, 12L, ~1
> > > 12L"
> > >
> > > Is there anything I am doing wrong ? I really need this function to
> > > complete my survival analysis... I would really appreciate if anyone
> could
> > > help me.
> >
> > I guess that an emergency solution is to be doing the whole analysis in R.
> >
> > Otherwise, you could try splitting up a bit your expression
> > r.plot(r.survfit(r.Surv(t,d)))
> > to see better were things are going wrong:
> > s = r.Surv(t,d)
> > sf = r.survfit(s)
> > plot(sf)
> >
> > The following has a chance to work (not tested):
> > survPlot = r.get("plot.survfit", envir=r.getNamespace("survival"))
> > survPlot(sf)
> >
> >
> > L.
> >
> > PS: An alternative to the NO_CONVERSION business might be coming in
> not-so-long.
> >
> >
> > > Thanks.
> > >
> > > Lore.
> > >
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