[ADMB Users] PBSadmb: an R package for ADMB

Thu Feb 5 00:52:21 PST 2009

Hi everyone - My colleague Rowan Haigh and I are pleased to announce our first release of PBSadmb, an R package for ADMB. So far, we've written it only for Windows. You can read about it and obtain it from http://code.google.com/p/pbs-software/. Although the User's Guide appears on the web site, I enclose it with this message for your convenience.

As we say on the web site: "We built PBSadmb so that we ourselves could use ADMB effectively. We believe that any R user who wants to run ADMB on a Windows platform will find PBSadmb a huge advantage for model development and analysis."

Last December, John Sibert asked for clarification about an R interface to ADMB. (See his message below.) The first two paragraphs of the Guide give our answer to this question:

"PBSadmb provides an R interface for developing models with the open version of a software package called AD Model Builder (ADMB). An R function handles every command normally associated with ADMB, including all steps required to make executable files. Consequently, the package enables an R user to handle all aspects of ADMB development with R script files. It includes a facility for ensuring that variable names match between the source file for ADMB (called a template) and a corresponding source file for R.

PBSadmb depends heavily on another R package PBSmodelling. We use this to implement a Graphical User Interface (GUI) that greatly facilitates ADMB model development. A user can edit code, test it rapidly, and inspect the results of analyses, including Markov chain Monte Carlo (MCMC) simulations. A new user can learn key aspects of ADMB template code with the examples provided."

For a much more complete answer, read the User's Guide (where Figure 1 shows the GUI), install the software, and try it. Steve Martell, please note that our GUI supports "fried eggs and beer" plots to represent Bayesian posterior samples.

Best wishes,
Jon

PS to staff at PBS - Rowan and I hope to demonstrate this software at PBS sometime next week. If you're interested, please try it on your computer. We'd appreciate some local feedback.

******************************************
Jon Schnute, Scientist Emeritus
Pacific Biological Station
3190 Hammond Bay Road
Nanaimo, BC V9T 6N7
CANADA

NEW email: Jon.Schnute at dfo-mpo.gc.ca 
 (formerly schnutej at pac.dfo-mpo.gc.ca)
******************************************

-----Original Message-----
From: John Sibert [mailto:sibert at hawaii.edu] 
Sent: December-15-08 12:10 PM
To: Schnute, Jon
Cc: Mark Maunder; Kery Marc; users at admb-project.org; Haigh, Rowan; Michael Prager
Subject: Re: [ADMB Users] AD Model Builder and R

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
> CANADA
>
> 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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