[R] Optim stripping attributes from relistable objects

[Prof Brian Ripley]

On Mon, 18 Aug 2008, Katharine Mullen wrote:

>>
>> The following code is inspired by the help file for the relist()
>> function (see?relist), which explicitly details how you can use a
>
> The example is in the 'Details' section and, indeed, it looks like it no
> longer works.

I don't think it ever did (after all there is a comment that dnorm does 
not have the parameters stated).

The subject line here illustrates the misunderstanding.  Optim *strips* 
nothing -- it creates a new object to pass to the function.  The help says

      Any names given to 'par' will be copied to the vectors passed to
      'fn' and 'gr'.

Note the use of 'copy' here.  You cannot assume that any other attributes 
will be copied, and this behaviour has not been changed (except to add 
names in March 2006, well before relist() was added), AFAICS.

>> relistable object in conjunction with optim to pass and reconstruct
>> complex parameter structures/groupings. The idea is that the optim()
>> function can only work with vectors, but in many cases you would like
>> to use a complex structure inside the objective function- relist is
>> one way to do that. The problem is that optim appears to be stripping
>> the attributes and therefore the example doesn't seem to run, giving
>> the error at the bottom.
>
> You can get around this by specifying skeleton for relist:
>
> rb.banana <- function(params) {
>    params <- relist(params, skeleton=list(x=NA,y=NA))
>    return( (1-params$x)^2 + 100*(params$y - params$x^2)^2)
> }
>
> ipar <-  as.relistable(list(x=5,y=0))
>
> initial.params <- unlist(ipar)
>
> xx <- optim(unlist(initial.params), rb.banana)
>
>>
>>> rb.banana <- function(params) {
>> +   #Params is initially a vector
>> +   cat("Params initially has the attributes:\n")
>> +   print(names(attributes(params)))
>> +   #Relisting it turns it into a list...
>> +   params <- relist(params)
>> +   cat("---------\n")
>> +   #..which can then be called in the standard list manner
>> +   return( (1-params$x)^2 + 100*(params$y - params$x^2)^2)
>> + }
>>>
>>> ipar            <-  as.relistable(list(x=5,y=0))
>>> initial.params  <-  unlist(ipar)
>>>
>>> #Test to see if rb.banana works properly in the "normal" case
>>> rb.banana(initial.params)
>> Params initially has the attributes:
>> [1] "names"    "skeleton"
>> ---------
>> [1] 62516
>>>
>>> #OK, that's good. How about with optim though?
>>> optim(initial.params,rb.banana)
>> Params initially has the attributes:
>> [1] "names"
>> Error in relist(params) :
>>   The flesh argument does not contain a skeleton attribute.
>> Either ensure you unlist a relistable object, or specify the skeleton
>> separately.
>>>
>>
>> What's going on here? Has this functionality been removed and the
>> documentation in relist() not updated? Or has the feature been broken?
>> Or have I misinterpreted something here (it wouldn't be the first
>> time!!)
>>
>> Am running R version 2.7.1 (2008-06-23) under windows.
>>
>> Cheers,
>>
>> Mark
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
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 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595