[FLR-list] size
Ernesto
ernesto.jardim at jrc.ec.europa.eu
Wed May 22 16:25:35 CEST 2013
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/
>>>>
>>>>
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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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>
>
> --
> 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>
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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