[ADMB Users] ADMB & R

Rubén Roa rroa at azti.es
Wed Aug 24 01:29:24 PDT 2011

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 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 

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?


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