R devel - Aug 2009 - Problem using model.frame with argument subset in own function

Dear List,

I am writing a formula method for a function in a package I maintain. I
want the method to return a data.frame that potentially only contains
some of the variables in 'data', as specified by the formula.

The problem I am having is in writing the function and wrapping it
around model.frame. Consider the following data frame:

dat <- data.frame(A = runif(10), B = runif(10), C = runif(10))

And the wrapper function:

foo <- function(formula, data = NULL, ..., subset = NULL,
                na.action = na.pass) {
    mt <- terms(formula, data = data, simplify = TRUE)
    mf <- model.frame(formula(mt), data = data, subset = subset,
                      na.action = na.action)
    ## real function would do more stuff here and pass mf on to
    ## other functions
    mf
}

This is how I envisage the function being called. The real world use
would have a data.frame with tens or hundreds of components where only a
few need to be excluded. Hence wanting formulas of the form below to
work.

foo(~ . - B, data = dat)

The aim is to return only columns A and C in an object returned by
model.frame. However, when I run the above, I get the following error:
> foo(~ A + B, data = dat)
Error in xj[i] : invalid subscript type 'closure'

I've tracked this down to the line in model.frame.default

    subset <- eval(substitute(subset), data, env)

After evaluating this line, subset contains:

Browse[1]> subset
function (x, ...) 
UseMethod("subset")
<environment: namespace:base>

Not NULL, and hence the error later on when calling the internal
model.frame code.

So the question is, what am I doing wrong?

If I leave the subset argument out of the definition of foo and rely
upon the default in model.frame.default, the function works as
expected. 

Perhaps the question should be, how do I modify foo() to allow it to
have a formal subset argument, passed to model.frame?

Any other suggestions gratefully accepted.

Thanks in advance,

G
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

On Sat, Aug 8, 2009 at 1:31 PM, Gavin Simpson<gavin.simpson at ucl.ac.uk>
wrote:
> Dear List,
> I am writing a formula method for a function in a package I maintain. I
> want the method to return a data.frame that potentially only contains
> some of the variables in 'data', as specified by the formula.
The usual way to call model.frame (the method that Thomas Lumley has
called "the standard, non-standard evaluation) is to match the call to
foo, replace the name of the function being called with
as.name("model.frame") and force an evaluation in the parent frame.
it looks like

    mf <- match.call()
    if (missing(data)) data <- environment(formula)
    ## evaluate and install the model frame
    m <- match(c("formula", "data", "subset",
"weights", "na.action", "offset"),
               names(mf), 0)
    mf <- mf[c(1, m)]
    mf$drop.unused.levels <- TRUE
    mf[[1]] <- as.name("model.frame")
    fr <- eval(mf, parent.frame())

The point of all of this manipulation is to achieve the kind of result
you need where the subset argument is evaluated in the correct
environmnent.
> The problem I am having is in writing the function and wrapping it
> around model.frame. Consider the following data frame:
>
> dat <- data.frame(A = runif(10), B = runif(10), C = runif(10))
>
> And the wrapper function:
>
> foo <- function(formula, data = NULL, ..., subset = NULL,
> ? ? ? ? ? ? ? ?na.action = na.pass) {
> ? ?mt <- terms(formula, data = data, simplify = TRUE)
> ? ?mf <- model.frame(formula(mt), data = data, subset = subset,
> ? ? ? ? ? ? ? ? ? ? ?na.action = na.action)
> ? ?## real function would do more stuff here and pass mf on to
> ? ?## other functions
> ? ?mf
> }
>
> This is how I envisage the function being called. The real world use
> would have a data.frame with tens or hundreds of components where only a
> few need to be excluded. Hence wanting formulas of the form below to
> work.
>
> foo(~ . - B, data = dat)
>
> The aim is to return only columns A and C in an object returned by
> model.frame. However, when I run the above, I get the following error:
>
>> foo(~ A + B, data = dat)
> Error in xj[i] : invalid subscript type 'closure'
>
> I've tracked this down to the line in model.frame.default
>
> ? ?subset <- eval(substitute(subset), data, env)
>
> After evaluating this line, subset contains:
>
> Browse[1]> subset
> function (x, ...)
> UseMethod("subset")
> <environment: namespace:base>
>
> Not NULL, and hence the error later on when calling the internal
> model.frame code.
>
> So the question is, what am I doing wrong?
>
> If I leave the subset argument out of the definition of foo and rely
> upon the default in model.frame.default, the function works as
> expected.
>
> Perhaps the question should be, how do I modify foo() to allow it to
> have a formal subset argument, passed to model.frame?
>
> Any other suggestions gratefully accepted.
>
> Thanks in advance,
>
> G
> --
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> ?Dr. Gavin Simpson ? ? ? ? ? ? [t] +44 (0)20 7679 0522
> ?ECRC, UCL Geography, ? ? ? ? ?[f] +44 (0)20 7679 0565
> ?Pearson Building, ? ? ? ? ? ? [e] gavin.simpsonATNOSPAMucl.ac.uk
> ?Gower Street, London ? ? ? ? ?[w] http://www.ucl.ac.uk/~ucfagls/
> ?UK. WC1E 6BT. ? ? ? ? ? ? ? ? [w] http://www.freshwaters.org.uk
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Gavin,

I ran into the same cryptic "invalid subscript type 'closure'"
message in
a slightly less complicated scenario, and wanted to post the cause in 
my case (the root cause is probably the same either way).

Similarly to your case, I was subsetting a data frame. I had a list
of variable names corresponding to columns in the frame. 
Unfortunately the variable name I had assigned to this list, var, 
coincided with the name of a base package function in R for variance.

When I attempted to subset df[, var], I got the 'closure' error message,
but if I renamed the list of variable names so the collision didn't occur,
e.g. df[, vars] instead of df[, var], it worked as expected.

Sincerely, 
Greg B. Hill


Gavin Simpson wrote:
> 
> Dear List,
> 
> I am writing a formula method for a function in a package I maintain. I
> want the method to return a data.frame that potentially only contains
> some of the variables in 'data', as specified by the formula.
> 
> The problem I am having is in writing the function and wrapping it
> around model.frame. Consider the following data frame:
> 
> dat <- data.frame(A = runif(10), B = runif(10), C = runif(10))
> 
> And the wrapper function:
> 
> foo <- function(formula, data = NULL, ..., subset = NULL,
>                 na.action = na.pass) {
>     mt <- terms(formula, data = data, simplify = TRUE)
>     mf <- model.frame(formula(mt), data = data, subset = subset,
>                       na.action = na.action)
>     ## real function would do more stuff here and pass mf on to
>     ## other functions
>     mf
> }
> 
> This is how I envisage the function being called. The real world use
> would have a data.frame with tens or hundreds of components where only a
> few need to be excluded. Hence wanting formulas of the form below to
> work.
> 
> foo(~ . - B, data = dat)
> 
> The aim is to return only columns A and C in an object returned by
> model.frame. However, when I run the above, I get the following error:
> 
>> foo(~ A + B, data = dat)
> Error in xj[i] : invalid subscript type 'closure'
> 
> I've tracked this down to the line in model.frame.default
> 
>     subset <- eval(substitute(subset), data, env)
> 
> After evaluating this line, subset contains:
> 
> Browse[1]> subset
> function (x, ...) 
> UseMethod("subset")
> <environment: namespace:base>
> 
> Not NULL, and hence the error later on when calling the internal
> model.frame code.
> 
> So the question is, what am I doing wrong?
> 
> If I leave the subset argument out of the definition of foo and rely
> upon the default in model.frame.default, the function works as
> expected. 
> 
> Perhaps the question should be, how do I modify foo() to allow it to
> have a formal subset argument, passed to model.frame?
> 
> Any other suggestions gratefully accepted.
> 
> Thanks in advance,
> 
> G
> -- 
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
>  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 
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