[Developers] Template functions and documentation

[dave fournier]

On 06/27/2014 11:39 AM, Mark Maunder wrote:

Anyway I looked up the Richards  (old mans memory) and it seems to be a 
logistic with an extra parameter,
whihc mean it has a lower asymptote.  I'm not sure one want that. Do you 
have a few example data sets I
can play with if I can;t thik of anything else useful to do.

      Dave


> Dave,
>
> The point is that the asymptotic length is controlled by the shape of 
> the growth curve and the fit to the young and intermediate aged fish. 
> For example, if you fit a vonB only to young fish that show linear 
> growth you get a very large Linf. The more flexible Richards curve 
> does better, but I don't think it bends over fast enough for the data 
> I have. I have created a composite growth model that is linear for 
> young fish and vonB for old fish, but I was wondering if there is a 
> better model out there that I don't know about.
>
> Mark
>
> *From:*dave fournier [mailto:davef at otter-rsch.com]
> *Sent:* Friday, June 27, 2014 11:34 AM
> *To:* Mark Maunder; developers at admb-project.org
> *Cc:* Alexandre Aires-Da-Silva; Carolina Minte-Vera
> *Subject:* Re: [Developers] Template functions and documentation
>
> On 06/27/2014 11:29 AM, Mark Maunder wrote:
>
> OK,  so the asymptotic length is important.  What is your point?
>
>     Dave
>
>     Thanks Dave,
>
>     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.
>
>     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.
>
>     Regards,
>
>     Mark
>
>     *From:*dave fournier [mailto:davef at otter-rsch.com]
>     *Sent:* Friday, June 27, 2014 11:11 AM
>     *To:* Mark Maunder; developers at admb-project.org
>     <mailto:developers at admb-project.org>
>     *Cc:* Alexandre Aires-Da-Silva; Carolina Minte-Vera
>     *Subject:* Re: [Developers] Template functions and documentation
>
>     On 06/27/2014 11:04 AM, Mark Maunder wrote:
>
>     Its hard to believe that Schnute and I figured out how to do this
>     properly almost 34 years ago
>     using punch cards on a machine with 18K user memory. Someone
>     really should figure out how to teach
>     people the importance of parameterizing nonlinear models in a
>     stable fashion.
>
>
>
>
>         Hi developers,
>
>         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".
>
>         Thanks,
>
>         Mark
>
>         /**
>
>         \defgroup CONTRIB Contributed libraries
>
>         */
>
>         /**
>
>         \ingroup CONTRIB
>
>         \defgroup CAPAM CAPAM created functions
>
>         */
>
>         #include <admodel.h>
>
>         /**  von Bertalanffy growth equation; constant objects.
>
>           \ingroup CAPAM
>
>           \brief Calculate the length from a given age based on the
>         von Bertalanffy equation. Written by Mark Maunder.
>
>           \param age age of individual, \f$a\f$.
>
>           \param Linf asymptotic length, \f$L_inf\f$.
>
>           \param K growth rate, \f$K\f$.
>
>           \param t0 age at zero length, \f$t_0\f$.
>
>           \return length predicted length of individual.
>         \f$L_inf*(1-exp(-K*(a-t0)))\f$.
>
>           */
>
>         template <typename type1, typename type1>
>
>         //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
>
>         //type1 is probably a long
>
>         //type2 is probably a dvariable (either a model parameter
>         (Linf K t0) or a derived variable (length))
>
>         //may need a type3, which is a dvar_vector if age and length
>         are vectors, where type 1 will be a vector
>
>         type1 vonB(const type1 &age, const type2 &Linf, const type2
>         &K, const type2 &t0)
>
>         {
>
>           type2 length = Linf*(1.-mfexp(-K*(age-t0)));
>
>           return (length);
>
>         }
>
>         //is length a bad word to use
>
>         //do we use ingroup for both groups and subgroups in doxygen
>         documentation
>
>         //should we use mfexp?
>
>         //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
>
>         //I couldn't work out how to put in the detailed description
>
>         //The equations did not work on my computer
>
>
>
>
>
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