Re: [R] Optim stripping attributes from relistable objects
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] namesskeleton
-
[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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and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, [EMAIL PROTECTED]
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, UKFax: +44 1865 272595
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Optim stripping attributes from relistable objects
On Mon, 18 Aug 2008, [EMAIL PROTECTED] wrote:
Ok - there is an easy work-around by just to passing the skeleton to
the objective function. But would it be possible to clarify this point
in the relist() help file please (specificaly the example I would
think), implies that attributes are copied through by optim and that
this is expected behaviour?
Already done. You can always check the current version on the SVN server,
here
https://svn.r-project.org/R/branches/R-2-7-branch/src/library/utils/man/relist.Rd
Thanks,
Mark
2008/8/18 Prof Brian Ripley - [EMAIL PROTECTED]
:
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] namesskeleton
-
[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
__
R-help@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.
__
R-help@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, [EMAIL PROTECTED]
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, UKFax: +44 1865 272595
--
Brian D. Ripley, [EMAIL PROTECTED]
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, UKFax: +44 1865 272595
__
R-help@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.
[R] Optim stripping attributes from relistable objects
Dear all,
The following code is inspired by the help file for the relist()
function (see?relist), which explicitly details how you can use a
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.
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$x^2)^2)
+ }
ipar- as.relistable(list(x=5,y=0))
initial.params - unlist(ipar)
#Test to see if rb.banana works properly in the normal case
rb.banana(initial.params)
Params initially has the attributes:
[1] namesskeleton
-
[1] 62516
#OK, that's good. How about with optim though?
optim(initial.params,rb.banana)
Params initially has the attributes:
[1] names
Error in relist(params) :
The flesh argument does not contain a skeleton attribute.
Either ensure you unlist a relistable object, or specify the skeleton
separately.
What's going on here? Has this functionality been removed and the
documentation in relist() not updated? Or has the feature been broken?
Or have I misinterpreted something here (it wouldn't be the first
time!!)
Am running R version 2.7.1 (2008-06-23) under windows.
Cheers,
Mark
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Optim stripping attributes from relistable objects
The following code is inspired by the help file for the relist()
function (see?relist), which explicitly details how you can use a
The example is in the 'Details' section and, indeed, it looks like it no
longer works.
relistable object in conjunction with optim to pass and reconstruct
complex parameter structures/groupings. The idea is that the optim()
function can only work with vectors, but in many cases you would like
to use a complex structure inside the objective function- relist is
one way to do that. The problem is that optim appears to be stripping
the attributes and therefore the example doesn't seem to run, giving
the error at the bottom.
You can get around this by specifying skeleton for relist:
rb.banana - function(params) {
params - relist(params, skeleton=list(x=NA,y=NA))
return( (1-params$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] namesskeleton
-
[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
__
R-help@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.
__
R-help@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.
