On Thu, Feb 21, 2008 at 9:19 AM, Lore Merdrignac <[EMAIL PROTECTED]> wrote:
>
> ________________________________
> > Date: Thu, 21 Feb 2008 15:03:52 +0100
>
>
> > From: [EMAIL PROTECTED]
> > To: rpy-list@lists.sourceforge.net
> > Subject: Re: [Rpy] help with the package survival
> >
> > 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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> > > > > > _______________________________________________
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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.
> > >
> > Date: Thu, 21 Feb 2008 15:03:52 +0100
>
> > From: [EMAIL PROTECTED]
> > To: rpy-list@lists.sourceforge.net
> > Subject: Re: [Rpy] help with the package survival
> >
> > May be importing rpy with
> >
> > import rpy
> >
> > does help ?
> >
>
> It was almost good ! But, since I am really lucky, an other error
> appears... There is still an error in the function survfit(), in spite of
> the "NO_CONVERSION".
>
> >>> import rpy
>
> >>> rpy.set_default_mode(rpy.NO_CONVERSION)
Do not use this until after doing the library() call.
> >>> from rpy import r
> >>> r.library("survival")
> Le chargement a nécessité le package : splines
> <Robj object at 0x009FD390>
>
Place the rpy.set_default_mode(rpy.NO_CONVERSION) HERE and see what you get.
> >>> 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)))
Let us know how it turns out....
Sean
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