difference in using with() and the "data" argument in glm (PR#9338)

I've redirected this reply from r-help to the bugs list.

On 11/3/2006 8:25 AM, vito muggeo wrote:

Dear all,
I am dealing with the following (apparently simple problem):
For some reasons I am interested in passing variables from a dataframe
to a specific environment, and in fitting a standard glm:

dati<-data.frame(y=rnorm(10),x1=runif(10),x2=runif(10))
KK<-new.env()
for(i in 1:ncol(dati)) assign(names(dati[i]),dati[[i]],envir=KK)
#Now the following two lines work correctly:
coef(glm(y~x1+x2,data=KK))
with(KK,coef(glm(y~x1+x2)))

#However if I write the above code inside a function, with() does not
appear to work..

ff<-function(Formula,Data,method=1){
     KK<-new.env()
     for(i in 1:ncol(Data)) assign(names(Data[i]),Data[[i]],envir=KK)
     o<-if(method==1) glm(Formula,data=KK) else with(KK,glm(Formula))
     o}

 > ff(y~x1+x2,dati,1) #it works

Call:  glm(formula = Formula, data = KK)
..[SNIP]..

 > ff(y~x1+x2,dati,2) #it does not

Error in eval(expr, envir, enclos) : object "y" not found

 >

Could anyone to explain such difference? I believed that
"with(data,glm(formula))" and "glm(formula,data)" were equivalent.

I think this is a bug in terms.formula.  Near the end it has

    environment(terms) <- environment(x)

where x is the formula.  Since "y" isn't defined in that environment, it
fails.  It would work for you with

    environment(terms) <- data

but see below.

A workaround that should work for you is to put

environment(Formula) <- KK

before the call to glm.

I'm not going to make the patch I suggest above, because I don't think
it's consistent with the expected behaviour of glm() in the case where
some of the terms in the formula are supposed to come from
environment(x), and some from "data".

I don't know how to handle that case properly:  I think it requires a
different search strategy than R employs (but I might be wrong).  This
isn't a problem with the workaround I suggested to you, because there
the parent of KK is environment(x), but that wouldn't be true in general.

Duncan Murdoch