> 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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> https://lists.sourceforge.net/lists/listinfo/rpy-list> >> >> >> > 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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