<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Joe,<br>
<br>
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.<br>
<br>
The location on CRAN, therefore, is not with R packages. On the main
CRAN page<br>
<br>
<a class="moz-txt-link-freetext" href="http://cran.r-project.org/">http://cran.r-project.org/</a><br>
<br>
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.<br>
<br>
The direct URL is <a class="moz-txt-link-freetext" href="http://cran.r-project.org/contrib/extra/x2r/">http://cran.r-project.org/contrib/extra/x2r/</a><br>
<br>
Hope that helps.<br>
<br>
Mike<br>
<br>
<br>
Joseph Thorley wrote on 12/15/2008 9:16 PM:
<blockquote cite="mid:004501c95f24$4d1234f0$e7369ed0$@ca" type="cite">
<pre wrap="">Hi Michael,
Also when I try and install the X2R.zip file that I downloaded from your
site (<a class="moz-txt-link-freetext" href="http://www.sefsc.noaa.gov/mprager/rinter.html">http://www.sefsc.noaa.gov/mprager/rinter.html</a>) 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
</pre>
<blockquote type="cite">
<pre wrap="">-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a> [<a class="moz-txt-link-freetext" href="mailto:users-bounces@admb">mailto:users-bounces@admb</a>-
project.org] On Behalf Of Michael H. Prager
Sent: December 15, 2008 1:33 PM
To: John Sibert
Cc: <a class="moz-txt-link-abbreviated" href="mailto:users@admb-project.org">users@admb-project.org</a>; 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:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Folks,
Perhaps someone could clarify what is meant by an "R interface to
</pre>
</blockquote>
<pre wrap="">ADMB"?
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<pre wrap="">might
</pre>
<blockquote type="cite">
<pre wrap="">be very useful: <a class="moz-txt-link-freetext" href="http://www.sefsc.noaa.gov/mprager/rinter.htm">http://www.sefsc.noaa.gov/mprager/rinter.htm</a>
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
</pre>
</blockquote>
<pre wrap="">an
</pre>
<blockquote type="cite">
<pre wrap="">ADMB IDE.
So, lets hear some feedback on what is meant by an "R interface to
</pre>
</blockquote>
<pre wrap="">ADMB".
</pre>
<blockquote type="cite">
<pre wrap="">Regards,
John
Schnute, Jon wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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 <a class="moz-txt-link-freetext" href="http://cran.r-project.org/">http://cran.r-project.org/</a>. 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
</pre>
</blockquote>
</blockquote>
<pre wrap="">work
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">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
(<a class="moz-txt-link-abbreviated" href="mailto:users@admb-project.org">users@admb-project.org</a>) 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: <a class="moz-txt-link-abbreviated" href="mailto:Jon.Schnute@dfo-mpo.gc.ca">Jon.Schnute@dfo-mpo.gc.ca</a> (formerly
<a class="moz-txt-link-abbreviated" href="mailto:schnutej@pac.dfo-mpo.gc.ca">schnutej@pac.dfo-mpo.gc.ca</a>)
******************************************
-----Original Message-----
From: Mark Maunder [<a class="moz-txt-link-freetext" href="mailto:mmaunder@iattc.org">mailto:mmaunder@iattc.org</a>] 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
</pre>
</blockquote>
</blockquote>
<pre wrap="">people
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">involved in the initial stages who have a lot more R knowledge than
</pre>
</blockquote>
</blockquote>
<pre wrap="">I
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">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 [<a class="moz-txt-link-freetext" href="mailto:marc.kery@vogelwarte.ch">mailto:marc.kery@vogelwarte.ch</a>] 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: <a class="moz-txt-link-abbreviated" href="mailto:bounce-3381192-3455202@list.cornell.edu">bounce-3381192-3455202@list.cornell.edu</a>
[<a class="moz-txt-link-freetext" href="mailto:bounce-3381192-3455202@list.cornell.edu">mailto:bounce-3381192-3455202@list.cornell.edu</a>]Im Auftrag von Mark
Maunder
Gesendet: Mittwoch, 10. Dezember 2008 21:31
An: <a class="moz-txt-link-abbreviated" href="mailto:euring-l@cornell.edu">euring-l@cornell.edu</a>
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
</pre>
</blockquote>
</blockquote>
<pre wrap="">Builder,
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">or ADMB, can now be downloaded without charge from a public website,
<a class="moz-txt-link-freetext" href="http://admb-project.org">http://admb-project.org</a>.
ADMB-based computer models are used globally to monitor populations
</pre>
</blockquote>
</blockquote>
<pre wrap="">of
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">many endangered and commercially valuable species, to develop
place-based resource management policies, and to reconstruct
</pre>
</blockquote>
</blockquote>
<pre wrap="">movements
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">of animals tracked with electronic tags. ADMB- based stock
</pre>
</blockquote>
</blockquote>
<pre wrap="">assessments
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
</blockquote>
<pre wrap="">of
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Fixed Effect, Random Effect, and Hierarchical Bayes Estimators for
</pre>
</blockquote>
</blockquote>
<pre wrap="">Mark
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Recapture Data Using AD Model Builder"
Please feel free to e-mail me if you have any questions about the
</pre>
</blockquote>
</blockquote>
<pre wrap="">ADMB
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">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
<a class="moz-txt-link-abbreviated" href="mailto:mmaunder@iattc.org">mmaunder@iattc.org</a>
<a class="moz-txt-link-freetext" href="http://iattc.org/iattc-staffMMaunder.htm">http://iattc.org/iattc-staffMMaunder.htm</a>
Spatial Analysis for Stock Assessment workshop 14-17 October 2008
<a class="moz-txt-link-freetext" href="http://www.fisheriesstockassessment.com/TikiWiki/tiki">http://www.fisheriesstockassessment.com/TikiWiki/tiki</a>-
</pre>
</blockquote>
</blockquote>
<pre wrap="">index.php?page=Spa
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">tial+Analysis+for+Stock+Assessment+2008
See the following website for information on fisheries stock
</pre>
</blockquote>
</blockquote>
<pre wrap="">assessment
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap=""><a class="moz-txt-link-freetext" href="http://www.fisheriesstockassessment.com/">http://www.fisheriesstockassessment.com/</a>
--------------------------------------------------------------------
</pre>
</blockquote>
</blockquote>
<pre wrap="">----
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">_______________________________________________
Users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Users@admb-project.org">Users@admb-project.org</a>
<a class="moz-txt-link-freetext" href="http://lists.admb-project.org/mailman/listinfo/users">http://lists.admb-project.org/mailman/listinfo/users</a>
</pre>
</blockquote>
</blockquote>
<pre wrap="">--
Michael Prager, Ph.D.
Senior Scientist
NOAA Southeast Fisheries Science Center
Beaufort, North Carolina 28516
<a class="moz-txt-link-freetext" href="http://www.sefsc.noaa.gov/mprager/">http://www.sefsc.noaa.gov/mprager/</a>
** Opinions expressed are personal, not official. No
** official endorsement of any product is made or implied.
_______________________________________________
Users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Users@admb-project.org">Users@admb-project.org</a>
<a class="moz-txt-link-freetext" href="http://lists.admb-project.org/mailman/listinfo/users">http://lists.admb-project.org/mailman/listinfo/users</a>
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Michael H. Prager, Ph.D.
Senior Scientist
NMFS Southeast Fisheries Science Center
Beaufort, North Carolina 28516 USA
<a class="moz-txt-link-freetext" href="http://www.sefsc.noaa.gov/mprager/">http://www.sefsc.noaa.gov/mprager/</a></pre>
</body>
</html>