[Rd] messing with ...

Christos Hatzis christos.hatzis at nuverabio.com
Wed Aug 13 18:38:27 CEST 2008

If I understand it correctly, one way would be to define a function to
specify the default options/arguments in the required order.

For example,

> mle.options <- function(method = "BFGS", lower = 0, upper = Inf,
+ list(method=method, lower=lower, upper=upper, hessian=hessian)
> mle.options()
[1] "BFGS"

[1] 0

[1] Inf


And the user can specify only the parameters that need non-default values:

> mle.options(method="CG")
[1] "CG"

[1] 0

[1] Inf


A similar function can be defined for the control parameters of optim.
Then all you need in the mle wrapper is: 

mle <- function(X, Y, optim.meth=mle.options(), optim.control=mle.control(),
...) {
	# preparatory steps
	optim(par, fn, method=optim.meth$method, lower=optim.meth$lower, 
		upper=optim.meth$upper, hessian=optim.meth$hessian,
		control = optim.control(), ...)

	# more stuff

Hope this helps.


> -----Original Message-----
> From: r-devel-bounces at r-project.org 
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Ben Bolker
> Sent: Wednesday, August 13, 2008 11:46 AM
> To: r-devel at r-project.org
> Subject: [Rd] messing with ...
>    I'm looking for advice on manipulating parameters that are 
> going to be passed through to another function.
>    Specifically, I am working on my version of "mle", which 
> is a wrapper for optim (among other optimizers).
> I would prefer not to replicate the entire argument list of 
> optim(), so I'm using ... to pass extra arguments through.
>    However:
>      the starting values are specified as a list, which means 
> that users can potentially specify them in any order (or at 
> least that's the way it works now -- one solution to the 
> problem I'm about to state is to insist that they specify the 
> parameters in the same order as they are given in the 
> arguments of the objective function).
>    However, there are other arguments (lower, upper, 
> control$parscale, control$ndeps) that should all be in the 
> same order as the objective function definition by the time 
> they get to optim()).  I can think of a few solutions:
>   (1) make the user specify them all in the right order (ugh)
>   (2) add all of them as explicit parameters to my function 
> so that I can rearrange them appropriately (ugh)
>   (3) mess with the ... argument before it gets passed 
> through to optim (impossible?)
>   (4) capture ... as arglist <- list(...), manipulate the 
> arguments as necessary, then pass them along to optim as
> do.call("optim",arglist) (ugh but maybe the best solution?)
>    any thoughts?
>   thanks
>    Ben Bolker

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