[ADMB Users] ADMB & R

Laurie lauriekell at googlemail.com
Wed Aug 24 07:25:48 PDT 2011

Great, I have a few examples that I was using for learning and maybe we 
should compare notes and maybe keep others informed.


On 08/24/2011 10:29 AM, Rubén Roa wrote:
> Hi Laurie,
> I am very interested and I think it would eventually become a standard 
> in nonlinear modeling: control everything from R but when it comes to 
> optimization, call an ADMB executable, a dll, or the C++ code created 
> by makeadm. This is the plan with my R package CatDyn, available on 
> CRAN. The current first version is a pure R implementation, that uses 
> the recent package optimx for greater flexibility in selecting a 
> numerical method and for numerical diagnostics such as the 
> Karesh-Kuhn-Tucker optimality criteria. The next version of the 
> package will give the choice to optimize using ADMB code instead of 
> R's numerical methods. The model procedure I have in mind is:
> 1) pre-processing of data, and selection of initial parameter values 
> with a toy version of the model in R,
> 2) optimization with ADMB code but controlled from R, with ADMB behind 
> the scene, and
> 3) capture of results, model diagnostics, and plotting results in R.
> So I'm very interested in your work. If I can be of help I'd be glad,
> Rubén
> Rubén H. Roa-Ureta, Ph. D.
> AZTI Tecnalia, Txatxarramendi Ugartea z/g,
> Sukarrieta, Bizkaia, SPAIN
> -----Original Message-----
> From: users-bounces at admb-project.org on behalf of Laurie
> Sent: Tue 8/9/2011 2:50 PM
> To: Users at admb-project.org
> Subject: [ADMB Users] ADMB & R
> Maybe this is not the right forum for my email but here goes.
> I am currently creating several R packages that use ADMB code; there are
> two ways of doing this i.e. use
>      1) an executable and text files (e.g. glmmADMB) or
>      2) create a dll or shared library
> There are advantages and disadvantages of both approaches, but there are
> also some things that could be
> done to make it easier to mix ADMB & R, i.e. creation of
>      a) make files that allow R & ADMB to be compiled together across
> all platforms
>      b) a set of standard R functions/methods for reading and writing R
> & ADMB files
>      c) adding to the basic ADMB output files to make it easier to
> create R objects
> There is also an R package Rcpp that makes it easier to create packages
> that combine R & C++, and this looks
> like something that could be "easily" adapted to make a generic R/ADMB
> interface.
> I am actively working on these things now, and might even be able to
> find funding for others. Is there any interest in
> pursuing this?
> Laurie
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