[Rd] Clarification on generic functions and methods

[Doran, Harold]

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