[FLR-list] size

Fri May 24 09:11:55 CEST 2013

I have some simple functions, e.g. the powell-wetherall method, calculation
of moments, ...
A class that implements the "Survival Estimation in Non-Equilibrium
situations" method. These all work on FLQuant and FLPar objects.
I propose to add these to https://github.com/ejardim/FLMethLen.git

I also have methods that get length/age data from SS and Multifan-Cl, these
could go there as well.
Would this be OK?

Laurie

On Wed, May 22, 2013 at 4:25 PM, Ernesto <ernesto.jardim at jrc.ec.europa.eu>wrote:

>  Yes, we (Iago and me) were discussing that issue. We shouldn't accept
> sparse data, the methods will have to check each bin and deal with the
> missing observations. If we force all lengths to be present we may loose a
> bit on space but the methods wont need to check the length of the bins and
> workout what is going on.
>
> Best
>
> EJ
>
>
> On 05/22/2013 04:18 PM, Laurie Kell wrote:
>
>  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
>> I-21027 Ispra (VA), Italy
>> Office : +39 0332 785311 <%2B39%200332%20785311>
>> Fax: +39 0332 789658 <%2B39%200332%20789658>
>> 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 789658
>>
>> 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 789658
>>
>> 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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>
>
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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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