Using $ accessor in GAM formula

Hmmm....

After reading that email four times, I think I see what you mean.

Checking for variables within particular scopes is probably one of the most
challenging things in R, and I would guess in other languages too.  In R
it's compounded by situations when you're writing a function to accept
variables as either a stand alone global variable, or as an element of a
data.frame or list.

I think this is a new problem, and I'll switch to the lengthier
data.frame[,'x'] syntax in gam for now.

By the way, about the $ accessors.  I can see why some people don't like
them, but they are a part of the language.  And, I think they're a good
part.  They make the code much more readable, and I have yet to make a
mistake using them (which makes me think that they can be used
responsibly).  Making code harder to read is its own source of error, and is
not something that I take lightly!

Thanks for the replies.  And, thank you Rolf for the detailed analysis.  Do
you think that your or I should submit a bug report to the package
maintainer?  I'm not sure how that works.  Very few of my challenges turn
out to be actual bugs, but I think this one is.

On Fri, May 6, 2011 at 4:53 AM, Berwin A Turlach
<Berwin.Turlach at gmail.com>wrote:

G'day Rolf,

On Fri, 06 May 2011 09:58:50 +1200
Rolf Turner <rolf.turner at xtra.co.nz> wrote:

but it's strange that the dodgey code throws an error with gam(dat1$y
~ s(dat1$x))  but not with gam(dat2$cf ~ s(dat2$s))

Something a bit subtle is going on; it would be nice to be able to
understand it.

Well,

R> traceback()
3: eval(expr, envir, enclos)
2: eval(inp, data, parent.frame())
1: gam(dat$y ~ s(dat$x))

So the lines leading up to the problem seem to be the following from
the gam() function:

       vars <- all.vars(gp$fake.formula[-2])
       inp <- parse(text = paste("list(", paste(vars, collapse = ","),
           ")"))
       if (!is.list(data) && !is.data.frame(data))
           data <- as.data.frame(data)



Setting

R> options(error=recover)

running the code until the error occurs, and then examining the frame
number for the gam() call shows that "inp" is
"expression(list( dat1,x ))" in your first example and
"expression(list( dat2,s ))" in your second example.  In both
examples, "data" is "list()" (not unsurprisingly).  When,

       dl <- eval(inp, data, parent.frame())

is executed, it tries to eval "inp", in both cases "dat1" and "dat2"
are found, obviously, in the parent frame.  In your first example "x" is
(typically) not found and an error is thrown, in your second example an
object with name "s" is found in "package:mgcv" and the call to eval
succeeds.  "dl" becomes a list with two components, the first being,
respectively, "dat1" or "dat2", and the second the body of the function
"s".  (To verify that, you should probably issue the command
"debug(gam)" and step through those first few lines of the function
until you reach the above command.)

The corollary is that you can use the name of any object that R will
find in the parent frame, if it is another data set, then that data
set will become the second component of "inp".  E.g.:

R> dat=data.frame(min=1:100,cf=sin(1:100/50)+rnorm(100,0,.05))
R> gam(dat$cf ~ s(dat$min))

Family: gaussian
Link function: identity

Formula:
dat$cf ~ s(dat$min)

Estimated degrees of freedom:
3.8925  total = 4.892488

GCV score: 0.002704789

Or

R> dat=data.frame(BOD=1:100,cf=sin(1:100/50)+rnorm(100,0,.05))
R> gam(dat$cf ~ s(dat$BOD))

Family: gaussian
Link function: identity

Formula:
dat$cf ~ s(dat$BOD)

Estimated degrees of freedom:
3.9393  total = 4.939297

GCV score: 0.002666985

Just out of pure academic interest. :-)

Hope your academic curiosity is now satisfied. :)

HTH.

Cheers,

       Berwin

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