[S] Labels wrong with lrm

Dear Jan,

Thank you very much for your excellent description of the
problem and the self-contained test code.  This is a
problem that I've been meaning to either document better
or solve for some time.  The root of the problem is with
the builtin S-Plus terms.inner function:

attr(terms.inner(asthma ~ pol(age,kx) + smok),'variables')

expression(age, kx, smok)

You can see that terms.inner inappropriately includes kx
as an independent variable as it does not know that
the first argument to pol is the special variable.
When a constant replaces kx, all is well.

As I am relying on the C code called by terms.inner to
do the job, I don't have a ready solution.  I would
be happy if someone comes up with a solution.  The
all.vars function in the R language has the same
limitation:

all.vars(asthma ~ pol(age,kx) + smok)
[1] "asthma" "age"   "kx"   "smok"

On Sat, 28 Jul 2001 fharrell at virginia.edu wrote:

Dear Jan,

Thank you very much for your excellent description of the
problem and the self-contained test code.  This is a
problem that I've been meaning to either document better
or solve for some time.  The root of the problem is with
the builtin S-Plus terms.inner function:

attr(terms.inner(asthma ~ pol(age,kx) + smok),'variables')

expression(age, kx, smok)

You can see that terms.inner inappropriately includes kx
as an independent variable as it does not know that
the first argument to pol is the special variable.
When a constant replaces kx, all is well.

As I am relying on the C code called by terms.inner to
do the job, I don't have a ready solution.  I would
be happy if someone comes up with a solution.  The
all.vars function in the R language has the same
limitation:

all.vars(asthma ~ pol(age,kx) + smok)
[1] "asthma" "age"   "kx"   "smok"

Well,

1) all.vars comes from S, and works the same under R.

2) I don't think it is a limitation.  all.vars is described as

Description:

     Return a character vector containing all the names which occur in
     an expression or call.

and kx is such a name.  Indeed, there is no way to know from just the
formula if it is length n-vector or a scalar.   I don't know what pol()
is, but guess it is from your library, in which case the interpretation
may well depend on where (if anywhere) that library is in the search path.

If you want special-purpose names in formulae (like strata) you need to
extend the formula-handling code.  Neither S4 nor R make that easy.

Brian

--
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Dear Jan,

Thank you very much for your excellent description of the
problem and the self-contained test code.  This is a
problem that I've been meaning to either document better
or solve for some time.  The root of the problem is with
the builtin S-Plus terms.inner function:

attr(terms.inner(asthma ~ pol(age,kx) + smok),'variables')

expression(age, kx, smok)

You can see that terms.inner inappropriately includes kx
as an independent variable as it does not know that
the first argument to pol is the special variable.
When a constant replaces kx, all is well.

f

av<-all.vars(f)
sapply(attr(terms(f),"term.labels"),function(term)

On Sat, 28 Jul 2001 fharrell at virginia.edu wrote:

Dear Jan,

Thank you very much for your excellent description of the
problem and the self-contained test code.  This is a
problem that I've been meaning to either document better
or solve for some time.  The root of the problem is with
the builtin S-Plus terms.inner function:

attr(terms.inner(asthma ~ pol(age,kx) + smok),'variables')

expression(age, kx, smok)

You can see that terms.inner inappropriately includes kx
as an independent variable as it does not know that
the first argument to pol is the special variable.
When a constant replaces kx, all is well.

I think this can't be fixed in general.  There is simply no way to know
whether pol(age,kx) contains two variables (like interaction(age,kx)) or
one variable, and if so, which is the variable and which the parameter.

The termplot() function has a function carrier.names() that guesses that
the first argument is the only variable, which is a useful heuristic until
you have log(0.5+x) as a term.

You can get the results of all.vars broken down by term like

f

I(log(0.5 + x)) ~ pol(age, kx) + ns(sbp, df) + factor(race, labels =
races) +
    sex

av<-all.vars(f)
sapply(attr(terms(f),"term.labels"),function(term)

av[match(all.vars(parse(text=term)),av)])
$"pol(age, kx)"
[1] "age" "kx"

$"ns(sbp, df)"
[1] "sbp" "df"

$"factor(race, labels = races)"
[1] "race"  "races"

$sex
[1] "sex"

(actually you only get the RHS of the formula, but that shouldn't be hard
to fix)

You might also look at how nlme and Jim Lindsey's nonlinear models
functions solve the question of whether a name refers to a a variable or a
parameter.

        -thomas

Thomas Lumley                   Asst. Professor, Biostatistics
tlumley at u.washington.edu        University of Washington, Seattle

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