[FLR-list] size

Wed May 22 16:18:46 CEST 2013

It could be due to sparse data and some size classes being missing. For
example going from a DB to a matrix.

Laurie

On Wed, May 22, 2013 at 4:05 PM, Ernesto <ernesto.jardim at jrc.ec.europa.eu>wrote:

>  Hi,
>
> That can be done already, the range name we use for age is "max" and "min"
> so we can use it directly for lengths.
>
> Not so sure about using different bin's size. Methods would need to check
> each bin size ...
>
> One doubt, when using different bin's size aren't you getting close to the
> age structure ? kind of slicing ?
>
> Best
>
> EJ
>
>
> On 05/22/2013 03:38 PM, Santiago Cerviño wrote:
>
>  Length based models usually group length classes for different causes.
> Sometimes you do not have the whole information; sometimes you need to
> simplify your model; you might need to make big groups for larger fish and
> small ones for medium size fish, etc. I think len bins should be user
> defined without constraints. It is also important to have the whole
> information (lower length and upper length) for each bin somewhere. This
> information will be needed. ****
>
> ** **
>
> Could work this idea that keeps consistency with FLR age names using only
> one number? For instance 5, 12, 20, 30 that means 5-12, 12-20, 20-30,
> 30-??. We would only need that maximum length is defined somewhere to know
> the size of the last bin (minage, maxage slots used for minlen maxlen).***
> *
>
> ** **
>
> Santi****
>
> ** **
>
> ** **
>  ------------------------------
>
> *De:* flr-list-bounces at lists.r-forge.r-project.org [
> mailto:flr-list-bounces at lists.r-forge.r-project.org<flr-list-bounces at lists.r-forge.r-project.org>]
> *En nombre de *Ernesto
> *Enviado el:* 22 May 2013 13:55
> *Para:* flr-list at r-forge.wu-wien.ac.at
> *Asunto:* Re: [FLR-list] size****
>
> ** **
>
> It won't work in several situations and IMO trying to find a solution for
> all doesn't work. We need to find a solution that works and implement
> methods for the others. We may try to be consistent with "age" and use
> [10,11) represented by "10" in the length names.
>
> Best
>
> EJ
>
> On 05/22/2013 02:43 PM, Laurie Kell wrote:****
>
>  but wont work with age slicing which is based on > & <=. ****
>
> Laurie****
>
> ** **
>
> On Wed, May 22, 2013 at 2:41 PM, Ernesto <ernesto.jardim at jrc.ec.europa.eu>
> wrote:****
>
> Hi,
>
> Yes, that is a problem that we need to sort out. I'm considering using
> midpoints. It has the advantage of being easy to coerce into numeric. In
> most cases that's what one needs for computations. Using boundaries will
> require other(s) operation(s) to get midpoints.
>
> Best
>
> EJ ****
>
>
>
> On 05/22/2013 02:23 PM, Laurie Kell wrote:****
>
>   There is an issue, boring but may be important to agree on now, i.e.
> labeling of length bins.****
>
> What does a length bin mean, i.e. if the "quant" dim represents length?
> and the values are 5, 10, ...?****
>
> In the mixdist package these are the righthand boundaries i.e. they
> represent (0,5] and (5,10]. But if they are the lefthand boundaries then
> they represent (5,10] and (10,INF]. Or they could be midpoints. One option
> would be to explicitly label the bins with the boundaries and then have
> methods for going backwards and forwards between parametric and
> non-parametric methods. Or to have an attribute that tracks the properties.
> ****
>
> Otherwise I can see a lot of time being wasted in stock assessments. well
> more than normal.****
>
> Laurie ****
>
> ** **
>
> On Wed, May 22, 2013 at 1:07 PM, Ernesto <ernesto.jardim at jrc.ec.europa.eu>
> wrote:****
>
> On 05/22/2013 12:02 PM, Ernesto wrote:****
>
> On 05/22/2013 11:34 AM, Sarah Kraak wrote:****
>
> Hi FLR-guys,
>
> As you know I am not an active FLR user, but last year I showed some
> interest in whether you have size-based stuff in FLR (see attached email).
> In the meanwhile Coilin Minto and myself have been working on something
> (also attached - note this is a draft of the idea; at the moment we are
> working on the code to get the final graphs out) which we are coding in R
> but which could/should eventually been done in FLR. Perhaps you are
> interested.
>
> Cheers,
> Sarah****
>
>
> Hi,
>
> Following Laurie's suggestion I've started a git repository for length
> methods in FLRhttps://github.com/ejardim/FLMethLen
>
> Maybe our first task should be o write down what we're doing with length
> data. Laurie's working on ALKs, so I guess you're interested in
> converting length frequencies to ages for stock assessment !? We (a4a)
> are working on OMs and how to generate them from length based data so
> that uncertainty on the growth model can be included in the MSE. Sarah
> and Colin Minto are working on selectivity. What else ?
>
> Best
>
> EJ****
>
> Hi,
>
> I've updated the readme to reflect the latest messages. ****
>
>
>
> EJ
>
> --
> Ernesto Jardim<ernesto.jardim at jrc.ec.europa.eu>
> Fisheries Scientist
> FISHREG – Scientific Support to Fisheries
> IPSC Maritime Affairs Unit
> EC Joint Research Center
> TP 051, Via Enrico Fermi 2749
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> Office : +39 0332 785311 <%2B39%200332%20785311>
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> Ernesto Jardim<ernesto.jardim at jrc.ec.europa.eu> <ernesto.jardim at jrc.ec.europa.eu>****
>
> Fisheries Scientist****
>
> FISHREG – Scientific Support to Fisheries****
>
> IPSC Maritime Affairs Unit****
>
> EC Joint Research Center****
>
> TP 051, Via Enrico Fermi 2749****
>
> I-21027 Ispra (VA), Italy****
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> Ernesto Jardim<ernesto.jardim at jrc.ec.europa.eu> <ernesto.jardim at jrc.ec.europa.eu>****
>
> Fisheries Scientist****
>
> FISHREG – Scientific Support to Fisheries****
>
> IPSC Maritime Affairs Unit****
>
> EC Joint Research Center****
>
> TP 051, Via Enrico Fermi 2749****
>
> I-21027 Ispra (VA), Italy****
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> Office : +39 0332 785311****
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> Fax: +39 0332 789658****
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> https://fishreg.jrc.ec.europa.eu/****
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> --
> Ernesto Jardim<ernesto.jardim at jrc.ec.europa.eu> <ernesto.jardim at jrc.ec.europa.eu>
> Fisheries Scientist
> FISHREG – Scientific Support to Fisheries
> IPSC Maritime Affairs Unit
> EC Joint Research Center
> TP 051, Via Enrico Fermi 2749
> I-21027 Ispra (VA), Italy
> Office : +39 0332 785311
> Fax: +39 0332 789658https://fishreg.jrc.ec.europa.eu/
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