[R] subsetting within a function using lme

[Andrew Robinson]

Hi Pam,

can you provide just enough code for us to reproduce the error on one
of the sample datasets included with lme?  No more and no less than
the minimum necessary, please.

I find it easier to debug when things are concrete :)

Thanks,

Andrew

On Wed, Jan 05, 2005 at 08:48:45AM +0800, Pamela McCaskie wrote:
> Thankyou for your help with subsetting within a function. I have now tried
> to apply the same theory in the framework of an lme as follows:
> 
> fit1.lme <- eval(substitute(lme(fixed=fixed, data=dataframe,
> random=random, correlation=corCAR1(form= corr), na.action=na.omit,
> subset=subset),list(subset=subs)))
> 
> but I get the following error:
> 
> Error in switch(mode(object), name = , numeric = , call = object,
> character = as.name(object),  :
>         [[ cannot be of mode logical
> 
> I'm not sure why. Can anyone help me with this?
> kind regards
> Pam
> 
> 
> 
> On Thu, 30 Dec 2004, Thomas Lumley wrote:
> 
> > On Thu, 30 Dec 2004, Pamela McCaskie wrote:
> > > And so my attempt to wrap a simple function around this looks like:
> > > test.fun <- function(formula, mydata, sub=NULL){
> > >  subs <- with(mydata, eval(sub))
> > >  fit.glm <- glm(formula=formula, data=mydata, family=binomial, subset=subs)
> > >  return(fit.glm)
> > > }
> > >
> > > But when I tested it out with
> > > test <- test.fun(y~x1+x2, mydata=testdata, sub=expression(SEX==0))
> > >
> > > I get:
> > > Error in "[.data.frame"(structure(list(N_ASTHMA = as.integer(c(0, 0, 0,  :
> > >        invalid subscript type
> >
> > I get a different error: it may be that you have an object called `subs`
> > in the global environment
> >
> > > I'm guessing that it's looking in the global environment for
> > > subs,
> >
> > More precisely, it is looking in environment where `formula` was created,
> > which happens to be the global environment.
> >
> > This is the sort of thing that happens with the fitting functions because
> > they go to such lengths to break the basic scoping of R.
> >
> >
> > You probably have to substitute() the evaluated subset into the glm call.
> >
> >    fit.glm <- eval(substitute(glm(formula=formula, data=mydata,
> >       family=binomial, subset=subset),list(subset=subs)))
> >
> >
> >  	-thomas
> >
> 
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