[FLR-list] size
Laurie
lauriekell at gmail.com
Mon Jun 17 12:56:11 CEST 2013
I have modified DESCRIPTION etc so that it compiles, as we are using it
for our albacore assessment this week. Mainly the io routines for MFCL
and SS.
Laurie
On 17/06/13 09:44, Ernesto Jardim wrote:
> 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 <mailto: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
> <mailto: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
>> <mailto: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>
>>> [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
>>> <mailto: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
>>>> <mailto: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
>>>>> <mailto: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
>>>>> <http://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
>>>>> <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/
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> flr-list mailing list
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>>>>>
>>>>>
>>>>>
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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 <tel:%2B39%200332%20785311>
>>> Fax:+39 0332 789658 <tel:%2B39%200332%20789658>
>>> https://fishreg.jrc.ec.europa.eu/
>>>
>>>
>>>
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>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list
>>
>>
>> --
>> 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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>>
>>
>>
>>
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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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