2008/2/21, Lore Merdrignac <[EMAIL PROTECTED]>:
>
> > Date: Thu, 21 Feb 2008 08:16:10 -0500
> > From: [EMAIL PROTECTED]
> > To: rpy-list@lists.sourceforge.net
> > Subject: Re: [Rpy] help with the package survival
>
> >
> > On Thu, Feb 21, 2008 at 8:08 AM, Lore Merdrignac <[EMAIL PROTECTED]>
> wrote:
> > >
> > > Hi,
> > > I have a problem with the package "survival" in rpy. I have to use the
> > > function survit() , and it works with R but not by calling R from python
> > > with rpy :
> > >
> > > >>> ss=r.survfit(s,weights=pds)
> > > Traceback (most recent call last):
> > > File "<interactive input>", line 1, in ?
> > > RPy_RException: Erreur dans UseMethod("survfit") : pas de méthode
> applicable
> > > pour "survfit"
> > >
> > > It seems that there is nothing implemented in rpy for this function...
> > > Do you know how I can manage this problem ? Have I made mistakes ? Or do
> > > you know what function I could use to have similar results ?
> >
> > Lore,
> >
> > You'll probably need to show how you construct "s", as it seems that
> > survfit is looking for a particular type of object. If "s" is not a
> > formula or a coxph object, that would explain the error. Note that
> > there is type-conversion going on in rpy, so even though "s" might
> > have started out as the correct type of object, it may not be by the
> > time you are calling the function here.
> >
> > Sean
> >
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>
>
> Thank you for your reply Sean.
>
> So, this is how I proceed with R :
> > d=rep(1,41)
> > t=c( rep(6,5), rep(9,3) , rep(12,24), rep(15,9) )
> > plot(survfit(Surv(t,d)))
> And I get a graph of life span.
>
> With rpy :
> >>> from rpy import r
> >>> r.library("survival")
> >>> 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 UseMethod("survfit") : pas de méthode applicable
> pour "survfit"
>
> Or :
> >>> s=r.Surv(t,d)
> >>> ss=r.survfit(s)
> Traceback (most recent call last):
> File "<interactive input>", line 1, in ?
> RPy_RException: Erreur dans UseMethod("survfit") : pas de méthode applicable
> pour "survfit"
>
> Is there a mistake...?
Not really... it is just that the conversion Sean was referring to
seems to be happening
(and is causing confusion - there are improvements coming on that
front, but that will
be for an other post).
You can try turning the conversion off with
rpy.set_default_mode(rpy.NO_CONVERSION)
prior to running your code.
> Thank you for your time Sean.
>
> Lore.
>
>
>
>
>
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