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<div class="moz-cite-prefix">On 06/27/2014 11:29 AM, Mark Maunder
wrote:<br>
<br>
OK, so the asymptotic length is important. What is your point?<br>
<br>
Dave<br>
<br>
<br>
</div>
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<p class="MsoNormal"><span style="color:#1F497D">Thanks Dave,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">We will
probably use a reparameterization like this when we do the
analysis. Right now I am trying to get the function coding
structure sorted out before I write too much code.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">If you have a
growth curve that is quite linear for the first few ages and
then bends over quickly, that would be useful. We have been
applying the Richards curve, but I think we might need to do
better. The issue is that the asymptotic length is quite
important when fitting to length composition data, but we
often don’t have much age (or tagging) data for old fish.
So, the asymptotic length is controlled by the shape of the
growth curve and the fit to the young and intermediate aged
fish. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Regards, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Mark <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<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";color:windowtext">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
dave fournier [<a class="moz-txt-link-freetext" href="mailto:davef@otter-rsch.com">mailto:davef@otter-rsch.com</a>]
<br>
<b>Sent:</b> Friday, June 27, 2014 11:11 AM<br>
<b>To:</b> Mark Maunder; <a class="moz-txt-link-abbreviated" href="mailto:developers@admb-project.org">developers@admb-project.org</a><br>
<b>Cc:</b> Alexandre Aires-Da-Silva; Carolina Minte-Vera<br>
<b>Subject:</b> Re: [Developers] Template functions and
documentation<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">On
06/27/2014 11:04 AM, Mark Maunder wrote:<br>
<br>
Its hard to believe that Schnute and I figured out how to do
this properly almost 34 years ago<br>
using punch cards on a machine with 18K user memory.
Someone really should figure out how to teach<br>
people the importance of parameterizing nonlinear models in
a stable fashion.<br>
<br>
<br>
<br>
<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi developers,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I am in the process or putting together a
model that will be used to evaluate several growth equations
so I thought I better try to use the ADMB project “approved”
approach for writing the functions. Below is a template
function and documentation for the von Bertalanffy growth
equation. I would appreciate any advice on doing this
“correctly”.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Mark<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">/**<o:p></o:p></p>
<p class="MsoNormal">\defgroup CONTRIB Contributed libraries<o:p></o:p></p>
<p class="MsoNormal">*/<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">/**<o:p></o:p></p>
<p class="MsoNormal">\ingroup CONTRIB <o:p></o:p></p>
<p class="MsoNormal">\defgroup CAPAM CAPAM created functions<o:p></o:p></p>
<p class="MsoNormal">*/<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">#include <admodel.h><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">/** von Bertalanffy growth equation;
constant objects.<o:p></o:p></p>
<p class="MsoNormal"> \ingroup CAPAM<o:p></o:p></p>
<p class="MsoNormal"> \brief Calculate the length from a
given age based on the von Bertalanffy equation. Written by
Mark Maunder.<o:p></o:p></p>
<p class="MsoNormal"> \param age age of individual, \f$a\f$.<o:p></o:p></p>
<p class="MsoNormal"> \param Linf asymptotic length,
\f$L_inf\f$.<o:p></o:p></p>
<p class="MsoNormal"> \param K growth rate, \f$K\f$.<o:p></o:p></p>
<p class="MsoNormal"> \param t0 age at zero length,
\f$t_0\f$.<o:p></o:p></p>
<p class="MsoNormal"> \return length predicted length of
individual. \f$L_inf*(1-exp(-K*(a-t0)))\f$.<o:p></o:p></p>
<p class="MsoNormal"> */<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">template <typename type1, typename
type1> <o:p></o:p></p>
<p class="MsoNormal">//can have multiple types so that they
are used below in variable definitions, they can differ
between function calls, but remain the same within a
function call
<o:p></o:p></p>
<p class="MsoNormal">//type1 is probably a long<o:p></o:p></p>
<p class="MsoNormal">//type2 is probably a dvariable (either a
model parameter (Linf K t0) or a derived variable (length))
<o:p></o:p></p>
<p class="MsoNormal">//may need a type3, which is a
dvar_vector if age and length are vectors, where type 1 will
be a vector<o:p></o:p></p>
<p class="MsoNormal">type1 vonB(const type1 &age, const
type2 &Linf, const type2 &K, const type2 &t0)<o:p></o:p></p>
<p class="MsoNormal">{<o:p></o:p></p>
<p class="MsoNormal"> type2 length =
Linf*(1.-mfexp(-K*(age-t0)));<o:p></o:p></p>
<p class="MsoNormal"> return (length);<o:p></o:p></p>
<p class="MsoNormal">} <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">//is length a bad word to use<o:p></o:p></p>
<p class="MsoNormal">//do we use ingroup for both groups and
subgroups in doxygen documentation<o:p></o:p></p>
<p class="MsoNormal">//should we use mfexp?<o:p></o:p></p>
<p class="MsoNormal">//what if age and length are vectors, but
age is a vector and length is a dvar_vector, do we need to
overload the type with one with three variable types<o:p></o:p></p>
<p class="MsoNormal">//I couldn't work out how to put in the
detailed description<o:p></o:p></p>
<p class="MsoNormal">//The equations did not work on my
computer <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif""><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Developers mailing list<o:p></o:p></pre>
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