[ADMB Users] AD Model Builder and R

Mon Dec 15 18:16:26 PST 2008

Hi Michael,

Also when I try and install the X2R.zip file that I downloaded from your
site (http://www.sefsc.noaa.gov/mprager/rinter.html) I get the error message

Error in gzfile(file, "r") : cannot open the connection
In addition: Warning message:
In gzfile(file, "r") :
  cannot open compressed file 'X2R/DESCRIPTION', probable reason 'No such
file or directory'

Best Wishes

Joe 

> -----Original Message-----
> From: users-bounces at admb-project.org [mailto:users-bounces at admb-
> project.org] On Behalf Of Michael H. Prager
> Sent: December 15, 2008 1:33 PM
> To: John Sibert
> Cc: users at admb-project.org; Kery Marc; Haigh, Rowan
> Subject: Re: [ADMB Users] AD Model Builder and R
> 
> All--
> 
> This is explain a little more about the software (ADMB2R) that
> coauthors
> and I have developed and that is available from my Web site, linked to
> by the ADMB Project site.  It is also available from CRAN.
> 
> Very briefly, ADMB2R provides an alternative to the REPORT_SECTION of
> ADMB.  In the ADMB template, a user writes a block of calls to
> high-level functions supplied by ADMB2R.  Those functions cause a
> special ASCII file to be written that can be imported by R's dget()
> function to form an R "list" object.  The calls are pretty simple,
> hardly more difficult than writing a standard output section. They do
> things like open the list, start a sublist (list within the list),
> store
> vectors or matrices, give names to the matrices, lists, and vectors,
> close the list, and that type of thing.
> 
> So the output we provide is entirely independent of the REPORT_SECTION.
> It turns out, though, a good way to write your first ADMB2R function
> calls is to start with an existing REPORT_SECTION and incrementally add
> parallel code for R-compatible output.
> 
> The assessment group here now uses this as the main output from ADMB.
> We write a short standard report section as well.
> 
> The advantages of this approach are that all data from any ADMB run can
> be transferred to R in a structured way, complete with names, comments,
> etc.  The output is complete and does not require parsing code (beyond
> the R parser itself).  It eliminates the need for multiple output files
> per run, and the data within the list can be structured and named to
> facilitate automated graphing.  (We have something called FishGraph,
> also available in the same places, that we use for that.)
> 
> ADMB2R is OS-independent and quick -- it is compiled with the template.
> However, due to quirks in ADMB, it works with only some compilers.  We
> have tested it with  Borland and gcc.  We hope that updates to ADMB
> will
> remove this compiler dependence so that ADMB2R can be used with any
> compiler.
> 
> The download of ADMB2R includes detailed documentation and examples.
> 
> Mike
> 
> 
> on 12/15/2008 3:10 PM John Sibert said the following:
> > 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.htm
> >
> > 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
> >>
> >
> 
> --
> Michael Prager, Ph.D.
> Senior Scientist
> NOAA Southeast Fisheries Science Center
> Beaufort, North Carolina  28516
> http://www.sefsc.noaa.gov/mprager/
> ** Opinions expressed are personal, not official.  No
> ** official endorsement of any product is made or implied.
> 
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