[ADMB Users] AD Model Builder and R

Gabor Grothendieck ggrothendieck at gmail.com
Mon Dec 15 13:04:13 PST 2008

Ideally an R interface to a package external to R allows one to
transparently use that package from within R using R commands as if the
package were itself written in R.  All inputs to the package provided
by the user would be R and all outputs back to the user would be R
although there might be translations going on underneath but they
would all be encapsulated within an interface that hides this from
the user.

There are several ways of doing this including (this is not

- using system calls from R and files, e.g. R2WinBUGS

- using interprocess communications, e.g. Ryacas

- using R's facilities to interface directly to C/C++ programs
  as discussed in the Writing Extensions Manual that comes with R,
  e.g. Rgraphviz (Bioconductor)

On Mon, Dec 15, 2008 at 3:10 PM, John Sibert <sibert at hawaii.edu> wrote:
> Hi Folks,
> Perhaps someone could clarify what is meant by an "R interface to ADMB"?
> Communication of data between R and admb applications is easily done with
> ascii files. This is what Anders Nielsen and I do for all of our track
> reconstruction software. Pierre Kleiber has written R packages to interact
> with MULTIFAN-CL. This approach is fast and platform independent. So I'm not
> sure what you are asking for.
> Mike Prager has created some software that he calls "middleware" for
> examining ADMB output. I haven't taken the opportunity to examine Mike's
> utilities, but the information on the website suggests it might be very
> useful:  http://www.sefsc.noaa.gov/mprager/rinter.html
> Creation of installation scripts and of an IDE for developing admb
> application are separate issues that should not depend on R. The Inno
> installer that Dave created is a promising start for Windows installations
> and will be developed further. Also we have had some positive results from
> preliminary tests of NetBeans for creation of an ADMB IDE.
> So, lets hear some feedback on what is meant by an "R interface to ADMB".
> Regards,
> John
> Schnute, Jon wrote:
>> Mark and colleagues - This note is a reply to a message forwarded to me by
>> Mark Maunder. I'm addressing a question by Marc Kery: "Any chance that
>> someone might develop an R interface [to ADMB]?"
>> You may or may not know that, with the help of colleagues here, I've
>> developed several packages for R in recent years. Three of them are
>> currently available on CRAN http://cran.r-project.org/. Each package name
>> begins with "PBS" for the Pacific Biological Station, where I still work as
>> a retired scientist.
>> We're now developing a package (PBSadmb) designed to support ADMB within
>> R. It will have a GUI interface, and it should make installation of ADMB
>> fairly easy for R users. Hopefully, it will work on all platforms that
>> support R, as long as the ADMB Project distributes the corresponding binary
>> libraries.
>> See the attached PDF file for a picture of the current (rather primitive)
>> interface. It may take a while for us to support multiple version of Open
>> ADMB, but I'll send a notice to all ADMB users (users at admb-project.org) when
>> PBSadmb is available.
>> Best wishes,
>> Jon
>> ******************************************
>> Jon Schnute, Scientist Emeritus
>> Pacific Biological Station
>> 3190 Hammond Bay Road
>> Nanaimo, BC V9T 6N7
>> NEW email: Jon.Schnute at dfo-mpo.gc.ca  (formerly
>> schnutej at pac.dfo-mpo.gc.ca)
>> ******************************************
>> -----Original Message-----
>> From: Mark Maunder [mailto:mmaunder at iattc.org] Sent: Wednesday, December
>> 10, 2008 4:13 PM
>> To: Kery Marc
>> Cc: Arni Magnusson; Schnute, Jon
>> Subject: RE: AD Model Builder now free
>> Marc,
>> I guess that there will be some form of integration with R because many of
>> the current ADMB users also use R. We have a couple of people involved in
>> the initial stages who have a lot more R knowledge than I do. Hopefully,
>> they will be motivated to make the necessary developments.
>> Currently there are DLLs for R, but few people use them.
>> Regards,
>> Mark
>> -----Original Message-----
>> From: Kery Marc [mailto:marc.kery at vogelwarte.ch] Sent: Wednesday, December
>> 10, 2008 12:37 PM
>> To: Mark Maunder
>> Subject: AW: AD Model Builder now free
>> Hi Mark,
>> any chance that someone might develop an R interface ?
>> Regards  --  Marc
>> -----Ursprüngliche Nachricht-----
>> Von: bounce-3381192-3455202 at list.cornell.edu
>> [mailto:bounce-3381192-3455202 at list.cornell.edu]Im Auftrag von Mark
>> Maunder
>> Gesendet: Mittwoch, 10. Dezember 2008 21:31
>> An: euring-l at cornell.edu
>> Betreff: AD Model Builder now free
>> The most widely used software package for the development of
>> state-of-the-art fisheries stock assessment methods, AD Model Builder,
>> or ADMB, can now be downloaded without charge from a public website,
>> http://admb-project.org.
>> ADMB-based computer models are used globally to monitor populations of
>> many endangered and commercially valuable species, to develop
>> place-based resource management policies, and to reconstruct movements
>> of animals tracked with electronic tags. ADMB- based stock assessments
>> are critical to the management of commercially important fisheries
>> stocks worth billions of dollars as well as ecologically sensitive
>> species, in the United States and
>> internationally. Every NOAA Fisheries Science Center uses the ADMB
>> software.
>> The recently released EURING 2007 proceedings has a manuscript
>> describing the use of ADMB for mark-recapture analysis: "Comparison of
>> Fixed Effect, Random Effect, and Hierarchical Bayes Estimators for Mark
>> Recapture Data Using AD Model Builder"
>> Please feel free to e-mail me if you have any questions about the ADMB
>> software
>> Mark Maunder
>> Inter-American  Tropical Tuna Commission
>> 8604 La Jolla Shores Drive
>> La Jolla, CA, 92037-1508, USA
>>  Tel: (858) 546-7027
>> Fax: (858) 546-7133
>> mmaunder at iattc.org
>> http://iattc.org/iattc-staffMMaunder.htm
>> Spatial Analysis for Stock Assessment workshop 14-17 October 2008
>> http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=Spa
>> tial+Analysis+for+Stock+Assessment+2008
>> See the following website for information on fisheries stock assessment
>> http://www.fisheriesstockassessment.com/
>>  ------------------------------------------------------------------------
>> _______________________________________________
>> Users mailing list
>> Users at admb-project.org
>> http://lists.admb-project.org/mailman/listinfo/users
> --
> Download ADModel Builder from http://admb-project.org
> In theory, there is no difference between theory and practice. In practice
> there is. Yogi Berra
> John Sibert, Manager
> Pelagic Fisheries Research Program
> University of Hawaii at Manoa
> 1000 Pope Road, MSB 313
> Honolulu, HI 96822
> United States
> Phone: (808) 956-4109
> Fax: (808) 956-4104
> Skype: john.sibert
> PFRP Web Site: http://www.soest.hawaii.edu/PFRP/
> email: sibert at hawaii.edu
> _______________________________________________
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