[FLR-list] size

[Ernesto Jardim]

Yes, sure. I will finish our things this week and post it as well. Not sure
it will work without the a4a pkg though ...

Best

EJ


On Fri, May 24, 2013 at 9:11 AM, Laurie Kell <lauriekell at googlemail.com>wrote:

> 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
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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
>>>
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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
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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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>>
>>
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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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