R devel - Nov 2009 - Clarification on generic functions and methods

I have constructed the following functions and need a little clarification:

### function to fit the model parameters
jml.fit <- function(dat, con = 1e-3, bias=FALSE, ...){
	do stuff ...
}

### default function which calls jml.fit
jml.default <- function(dat, con = 1e-3, bias=FALSE, ...){
	result <- jml.fit(dat, con = 1e-3, bias)
	result$call <- match.call()
	class(result) <- "jml"
	result
}

### Function to make use of formula
jml.formula <- function(formula, data, na.action, subset, ...){
	mf <- match.call(expand.dots = FALSE)
    m <- match(c("formula", "data",
"na.action", "subset"), names(mf), 0L)
    mf <- mf[c(1L, m)]
    mf$drop.unused.levels <- TRUE
    mf[[1L]] <- as.name("model.frame")
    mf <- eval(mf, parent.frame())
	mt <- attr(mf, "terms")
	dat <- mf
	result <- jml.default(dat, ...)
	result$call <- match.call()
	result$formula <- formula
	result
}

### and the generic function 
jml <- function(dat, con = 1e-3, bias=FALSE, ...) UseMethod("jml")

Writing R Extensions states, "If the generic specifies defaults, all
methods should use the same defaults."

In my example above, the generic function has 2 defaults: one for argument con
and another bias. I'm a little confused on exactly how the generic function
should be structured for proper package development.

I think the options are:

1) jml <- function(dat, con = 1e-3, bias=FALSE, ...)
UseMethod("jml")
2) jml <- function(x, con = 1e-3, bias=FALSE, ...) UseMethod("jml")
3) jml <- function(formula, data, na.action, subset, con = 1e-3, bias =
FALSE, ...) UseMethod("jml")

I'm inclined to believe #3 is correct because the .Rd page needs to reflect
the args in this function, is that right? Then, this generic function would
include the formula, data, na.action, and subset and it includes the proper
defaults as the other functions.

Thank you
Harold
> sessionInfo()
R version 2.10.0 (2009-10-26) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] scoreFoo_1.1   MiscPsycho_1.4 statmod_1.4.1 

loaded via a namespace (and not attached):
[1] tools_2.10.0

Using

jml <- function(...) UseMethod("jml")

will do.

/Henrik


On Wed, Nov 11, 2009 at 4:26 PM, Doran, Harold <HDoran at air.org>
wrote:
> I have constructed the following functions and need a little clarification:
>
> ### function to fit the model parameters
> jml.fit <- function(dat, con = 1e-3, bias=FALSE, ...){
> ? ? ? ?do stuff ...
> }
>
> ### default function which calls jml.fit
> jml.default <- function(dat, con = 1e-3, bias=FALSE, ...){
> ? ? ? ?result <- jml.fit(dat, con = 1e-3, bias)
> ? ? ? ?result$call <- match.call()
> ? ? ? ?class(result) <- "jml"
> ? ? ? ?result
> }
>
> ### Function to make use of formula
> jml.formula <- function(formula, data, na.action, subset, ...){
> ? ? ? ?mf <- match.call(expand.dots = FALSE)
> ? ?m <- match(c("formula", "data",
"na.action", "subset"), names(mf), 0L)
> ? ?mf <- mf[c(1L, m)]
> ? ?mf$drop.unused.levels <- TRUE
> ? ?mf[[1L]] <- as.name("model.frame")
> ? ?mf <- eval(mf, parent.frame())
> ? ? ? ?mt <- attr(mf, "terms")
> ? ? ? ?dat <- mf
> ? ? ? ?result <- jml.default(dat, ...)
> ? ? ? ?result$call <- match.call()
> ? ? ? ?result$formula <- formula
> ? ? ? ?result
> }
>
> ### and the generic function
> jml <- function(dat, con = 1e-3, bias=FALSE, ...)
UseMethod("jml")
>
> Writing R Extensions states, "If the generic specifies defaults, all
methods should use the same defaults."
>
> In my example above, the generic function has 2 defaults: one for argument
con and another bias. I'm a little confused on exactly how the generic
function should be structured for proper package development.
>
> I think the options are:
>
> 1) jml <- function(dat, con = 1e-3, bias=FALSE, ...)
UseMethod("jml")
> 2) jml <- function(x, con = 1e-3, bias=FALSE, ...)
UseMethod("jml")
> 3) jml <- function(formula, data, na.action, subset, con = 1e-3, bias =
FALSE, ...) UseMethod("jml")
>
> I'm inclined to believe #3 is correct because the .Rd page needs to
reflect the args in this function, is that right? Then, this generic function
would include the formula, data, na.action, and subset and it includes the
proper defaults as the other functions.
>
> Thank you
> Harold
>
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United
States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
>
> other attached packages:
> [1] scoreFoo_1.1 ? MiscPsycho_1.4 statmod_1.4.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>