[R] subsetting within a function using lme

[Pamela McCaskie]

Here you go
A simplified version of the function looks like this:

test.fun <- function(fixed, random, mydata, sub=NULL){

  library(nlme)
  subs <- with(mydata, eval(sub))
  fit.lme <- eval(substitute(lme(fixed=fixed, data=mydata, random=random,
na.action=na.omit, subset=subset),list(subset=subs)))

  return(fit.lme)
}

So using the Orthodont dataset I tried:

test <- snp.long(fixed=distance~age, random=~1|Subject, mydata=Orthodont,
sub=expression(Sex=="Male"))

and get that error.
Error in switch(mode(object), name = , numeric = , call = object,
character = as.name(object),  :
        [[ cannot be of mode logical

Thanks for your help

> 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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