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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Arni and Chris,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for the information about Bugs.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Attached is a paper that describes the use of software programs
in fisheries stock assessment. It agrees with much of what you have been
discussing. It also talks about other software that is also used in combination
with ADMB. I personally use ADMB for estimation, R for graphics, and Excel for
simple calculations and model checking. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Mark<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;color:#1F497D'>Mark Maunder <o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Head of the Stock Assessment
Program<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Inter-American Tropical
Tuna Commission<br>
8604 La Jolla Shores Drive<br>
La Jolla, CA, 92037-1508, USA<br>
<br>
Tel: (858) 546-7027<br>
Fax: (858) 546-7133<br>
<a href="mailto:mmaunder@iattc.org">mmaunder@iattc.org</a><br>
</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'><a
href="http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=Mark+Maunder">http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=Mark+Maunder</a></span><span
style='font-size:11.0pt;color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;color:#1F497D'>Visit the AD
Model Builder project at<br>
<a href="http://admb-project.org/"><span style='color:#810081'>http://admb-project.org/</span></a></span><span
style='color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;color:#1F497D'>See the
following website for information on fisheries stock assessment<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;color:#1F497D'><a
href="http://www.fisheriesstockassessment.com/">http://www.fisheriesstockassessment.com/</a></span><span
style='font-size:11.0pt;color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p></o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
users-bounces@admb-project.org [mailto:users-bounces@admb-project.org] <b>On
Behalf Of </b>Chris Gast<br>
<b>Sent:</b> Wednesday, June 16, 2010 12:11 PM<br>
<b>To:</b> Arni Magnusson<br>
<b>Cc:</b> r-help@r-project.org; users@admb-project.org<br>
<b>Subject:</b> Re: [ADMB Users] an alternative to R for nonlinear stat models<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Arni (and others),<o:p></o:p></p>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>My dissertation work involves use (and extension) of models
of the same ilk (sometimes exactly the same) as those described by Nancy Gove
and John Skalski in their 2002 article. I began with R, and moved to my
own home-brewed C/C++ programs for the sake of of speed when fitting models and
real and simulated data. In addition, we found that the estimated
standard errors (based on the inverse hessian output from optim()) were very
sensitive to tolerance criteria--often changing orders of magnitude.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>I have recently made the move to ADMB to make use of the
capabilities for mixed effect models. One of my current tasks involves
simulating data (in R), fitting models in ADMB via the shell() command in R,
and importing .rep files into R for processing results of multiple simulations.
In this respect, I too describe my working environment as "R with
ADMB," and understand the relative benefits of this setup. For these
specific types of models, I've found ADMB to be irreplaceable. Similarly,
I could not easily summarize simulation results without R; both are vital
components to the work I'm doing.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>With respect to your benchmarking suggestion: I have
many implementations of models for real and simulated data in both R and ADMB
(past and current iterations of my work on the models described above), and may
be able to complete some of this work alongside my own work, although I don't
yet claim that either my R or ADMB implementations are completely optimized for
speed.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Chris<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>-----------------------------<br>
Chris Gast<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>University of Washington<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'>Quantitative Ecology and
Resource Management<br>
<a href="mailto:cmgast@gmail.com">cmgast@gmail.com</a><br>
<br>
<o:p></o:p></p>
<div>
<p class=MsoNormal>On Wed, Jun 16, 2010 at 11:39 AM, Arni Magnusson <<a
href="mailto:arnima@hafro.is">arnima@hafro.is</a>> wrote:<o:p></o:p></p>
<p class=MsoNormal>As far as I can tell, Gove et al. (2002) might be a good
example for benchmarking the optimization performance of R vs. ADMB. It would
be great if expert R users/developers could tweak Beni's model so that the
performance comparison is valid.<br>
<br>
The main purpose is not to see which is faster or more reliable, but to
quantify how much performance is gained by moving from R to ADMB.<br>
<br>
I have just typed and uploaded an excerpt from an old but thorough benchmark,
where ADMB outperformed Gauss, Matlab, and S-Plus (<a
href="http://admb-project.org/community/benchmarks/optimization" target="_blank">http://admb-project.org/community/benchmarks/optimization</a>).
The benchmark was performed in 1997 and an update would be very valuable, as
software and hardware have improved since then.<br>
<br>
R is an interpreted language that can do just about anything. ADMB is a
compiled language (thin layer on top of C++) that does optimization and nothing
else. I don't think it is a realistic goal for R to match the optimizing
performance of ADMB. I use R for most of my work, but crunch numbers with ADMB
when computational speed and flexibility become an issue.<br>
<br>
As an analogy, data frames in R are great, along with functions like
aggregate(), apply(), merge(), and xtabs(). But when the tables are too large
and too many, it's time to delegate the problem to a relational database.<br>
<br>
In the case of model X, which is already implemented in R, it may take half an
hour or half a month to convert it to ADMB, and the payoff depends on how often
the model needs to be run. In the case of model Y, which is not yet
implemented, some users may be quicker to implement it in R than in ADMB, so
again it would be good to have an idea about the relative performance gain.
Model Z may not run at all in R, due to its size and complexity.<br>
<br>
Although I started this email with "R vs. ADMB", my daily working
environment is better described as "R and ADMB". I'm a regular
contributor to both R (4 packages and a couple of functions in the base
packages) and ADMB (dev core team). Others have contributed R packages to
interface with ADMB (<a
href="http://admb-project.org/community/admb-meeting-march-29-31/InterfacingADMBwithR.pdf/at_download/file"
target="_blank">http://admb-project.org/community/admb-meeting-march-29-31/InterfacingADMBwithR.pdf/at_download/file</a>),
but for many the interface is just reading and writing text files.<br>
<br>
I fully appreciate the comfort and efficiency of the R working environment, and
the benefits of performing most tasks inside the same environment. But the R
community has no need to be on the defense against ADMB, any more than against
relational databases. If you work with computationally intensive models, I
encourage you to try out ADMB (<a href="http://admb-project.org" target="_blank">admb-project.org</a>,
free software) and hopefully end up contributing ideas and/or code.<br>
<br>
Best regards,<br>
<br>
Arni<br>
<br>
<br>
P.S. Phew. Future emails mentioning ADMB on r-help can be more brief and to the
point, citing this message for details.<br>
<br>
<br>
Windows ADMB-IDE installer<br>
<a href="http://code.google.com/p/admb-project/downloads/list?q=ide*exe"
target="_blank">http://code.google.com/p/admb-project/downloads/list?q=ide*exe</a><br>
<br>
Windows, Linux, and Mac OS standalone<br>
<a href="http://code.google.com/p/admb-project/downloads/list?q=windows"
target="_blank">http://code.google.com/p/admb-project/downloads/list?q=windows</a><br>
<a href="http://code.google.com/p/admb-project/downloads/list?q=linux"
target="_blank">http://code.google.com/p/admb-project/downloads/list?q=linux</a><br>
<a href="http://code.google.com/p/admb-project/downloads/list?q=macos"
target="_blank">http://code.google.com/p/admb-project/downloads/list?q=macos</a><br>
<br>
ADMB modes for various editors, including Emacs and Vim<br>
<a href="http://admb-project.org/community/editing-tools" target="_blank">http://admb-project.org/community/editing-tools</a><br>
_______________________________________________<br>
Users mailing list<br>
<a href="mailto:Users@admb-project.org" target="_blank">Users@admb-project.org</a><br>
<a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><o:p></o:p></p>
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