[R] subset and lme

[Thomas Lumley]

On Wed, 16 Jun 2004, Todd Ogden wrote:

> Version of R - the problem is both on 1.8 and 1.9.
>
> Version of nlme - 3.1-48
>
> It turns out that the problem is deeper than what I just posted -- in
> other calls to lme, I get error messages saying objects not found,
> even when the objects in question are created explicitly before the
> lme function call or even arguments to the function that's making the
> lme calls!  I can do print(obj) just before the lme call, but then if
> obj is used in the lme call, it's not found.
>

Is this inside a function or at the R prompt?

	-thomas





> Todd
> to166 at columbia.edu
>
> >
> > Todd Ogden wrote:
> >
> > > I'm puzzled by the following problem, which appears when
> > > attempting to run an analysis on part of a dataset:
> > >
> > > If I try:
> > >
> > >   csubset <- dat$Diagnosis==0
> > >   cont <- lme(fixed=cform,
> > >                    random = ~1|StudyName,
> > >                       data=dat,subset=csubset,na.action=na.omit)
> > >
> > > Then I get:
> > >
> > > Error in eval(expr, envir, enclos) : Object "csubset" not found
> > >
> > > But if I do instead:
> > >
> > >   cdat <- dat[dat$Diagnosis==0,]
> > >   cont <- lme(fixed=cform,
> > >                    random = ~1|StudyName,
> > >                       data=cdat,na.action=na.omit)
> > >
> > > Then everything is fine.
> > >
> > > I'm puzzled that the object can't be found.  Maybe I'm
> > > overlooking something obvious?
> > >
> >
> > Todd,
> >    What version of R/nlme? I just tried the following:
> >
> > library(nlme)
> > data(Orthodont)
> > csubset <- Orthodont$Sex == "Male"
> > fm1 <- lme(distance ~ age, data = Orthodont,
> >             random = ~ 1, subset = csubset)
> > fm2 <- lme(distance ~ age, data = Orthodont,
> >             random = ~ 1, subset = Sex == "Male")
> > fm3 <- lme(distance ~ age, data = Orthodont[csubset, ],
> >             random = ~ 1)
> >
> >  > R.version.string
> > [1] "R version 1.9.0, 2004-05-06"
> > R> library(help = "nlme")
> >
> > 		Information on Package 'nlme'
> >
> > Description:
> >
> > Package: nlme
> > Version: 3.1-48
> > Date: 2004/01/14
> > <snip>
> >
> > --sundar
> >
> >
> >
> >
>
>
> --
>
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Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle