[ADMB Users] PBSadmb: an R package for ADMB

Fri Feb 6 11:35:10 PST 2009

It will be fascinating to see the package running on non-Windows platform.

Shige

On Thu, Feb 5, 2009 at 12:52 AM, Schnute, Jon <Jon.Schnute at dfo-mpo.gc.ca>wrote:

> 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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>
>
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