[ADMB Users] AD Model Builder and R

Mon Dec 15 20:19:55 PST 2008

Hi Mike,

Thanks for the clarification.

Best Wishes

Joe

From: Michael Prager [mailto:Mike.Prager at noaa.gov] 
Sent: December 15, 2008 7:27 PM
To: joethorley at poissonconsulting.ca
Cc: 'John Sibert'; users at admb-project.org; 'Kery Marc'; 'Haigh, Rowan'
Subject: Re: [ADMB Users] AD Model Builder and R

Joe,

I am guessing that the issue you experienced is from trying to install
ADMB2R (which as you say is part of X2R) as an R package.  Because it is a
subroutine library for ADMB, it is not structured as an R package. So you
should just unzip the file and see what's there.

The location on CRAN, therefore, is not with R packages.  On the main CRAN
page

http://cran.r-project.org/

is a menu at the left.  Under the "Software" heading, click on "Other".
About halfway down the page is X2R, which includes ADMB2R.  When you are at
the CRAN X2R page, there is an HTML overview file that can be loaded &
installation packages that can be downloaded.

The direct URL is http://cran.r-project.org/contrib/extra/x2r/

Hope that helps.

Mike

Joseph Thorley wrote on 12/15/2008 9:16 PM: 

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/

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--
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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-- 
Michael H. Prager, Ph.D.
Senior Scientist
NMFS Southeast Fisheries Science Center
Beaufort, North Carolina  28516  USA
http://www.sefsc.noaa.gov/mprager/
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