May be importing rpy with
import rpy
does help ?
2008/2/21, Lore Merdrignac <[EMAIL PROTECTED]>:
>
> > Date: Thu, 21 Feb 2008 14:48:10 +0100
> > From: [EMAIL PROTECTED]
>
> > To: rpy-list@lists.sourceforge.net
> > Subject: Re: [Rpy] help with the package survival
> >
> > 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.
> >
>
> I have just tried but it does not seem to work ... Below there is what I
> got :
>
> >>> rpy.set_default_mode(rpy.NO_CONVERSION)
> Traceback (most recent call last):
> File "<interactive input>", line 1, in ?
> NameError: name 'rpy' is not defined
>
> >>> r.set_default_mode(r.NO_CONVERSION)
> Traceback (most recent call last):
> File "<interactive input>", line 1, in ?
> File "C:\Python24\Lib\site-packages\rpy.py", line 302, in
> __getattr__
> return self.__getitem__(name)
> File "C:\Python24\Lib\site-packages\rpy.py", line 306, in
> __getitem__
> obj = self.__dict__[name] = self.__dict__.get(name, self.get(name))
> RPy_RException: Erreur dans function (x, pos = -1, envir =
> as.environment(pos), mode = "any", :
> variable "set.default.mode" introuvable
>
> >>> r.set_default_mode(rpy.NO_CONVERSION)
> Traceback (most recent call last):
> File "<interactive input>", line 1, in ?
> File "C:\Python24\Lib\site-packages\rpy.py", line 302, in
> __getattr__
> return self.__getitem__(name)
> File "C:\Python24\Lib\site-packages\rpy.py", line 306, in
> __getitem__
> obj = self.__dict__[name] = self.__dict__.get(name, self.get(name))
> RPy_RException: Erreur dans function (x, pos = -1, envir =
> as.environment(pos), mode = "any", :
> variable "set.default.mode" introuvable
>
> Is there any other solution :$ ? Thanks for answering.
> Lore.
>
>
> >
> > > Thank you for your time Sean.
> > >
> > > Lore.
> > >
> > >
> > >
> > >
> > >
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> >
> >
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