[ADMB Users] AD Model Builder and R

Schnute, Jon Jon.Schnute at dfo-mpo.gc.ca
Sat Dec 13 19:58:10 PST 2008

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 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


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.



-----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
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,

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

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

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

Spatial Analysis for Stock Assessment workshop 14-17 October 2008

See the following website for information on fisheries stock assessment

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