> 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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> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/> > > > >
> _______________________________________________> > > > > rpy-list mailing
> list> > > > > rpy-list@lists.sourceforge.net> > > > >
> 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.> >> 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)>>> from rpy import
>>> r>>> r.library("survival")Le chargement a nécessité le package :
>>> splines<Robj object at 0x009FD390>>>> 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,
>>> ~112L"
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