[FLR-list] size

Wed May 22 15:38:27 CEST 2013

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] 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 <tel:%2B39%200332%20785311> 
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	-- 
	Ernesto Jardim<ernesto.jardim at jrc.ec.europa.eu> <mailto: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 <tel:%2B39%200332%20785311> 
	Fax: +39 0332 789658 <tel:%2B39%200332%20789658> 
	https://fishreg.jrc.ec.europa.eu/

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-- 
Ernesto Jardim<ernesto.jardim at jrc.ec.europa.eu> <mailto: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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