[FLR-list] ssb constraint with FLash
Iago MOSQUEIRA (JRC)
iago.mosqueira at jrc.ec.europa.eu
Mon Oct 27 11:30:08 CET 2014
Looking into it, and yes, it works with ple4, but not with Clara's
dataset... It settles for a value of ssb that is not yet the limit,
despite haven't achieved the F target.
Iago
On 27/10/14 10:56, laurie wrote:
> Bad documentation!
>
> This works, Although I would not recommend the use of use stf anymore.
> Rather I fit an FLBRP object and then use the vectors in that to set the
> projection values, that way reference points and projections are
> consistent.
>
> data(ple4)
>
> ple4 <- stf(ple4,3)
>
> maxF <-fwdControl(data.frame(year=2009,val=0.8,quantity="f"))
> # an example with high F that decreases biomass a lot
>
> ple4=fwd(ple4,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residuals=
> FLQuant(3500000,dimnames=list(year=2009:2011)))
>
> fbar(ple4)[,"2009"]
>
> maxF <-fwdControl(data.frame(year=c(2009,2009),
> val =c(0.8,NA),
> min =c(NA,350000),
> quantity=c("f","ssb")))
>
> ple4=fwd(ple4,ctrl=maxF,
> sr=list(model="mean",params=FLPar(1)),
> sr.residuals=FLQuant(3500000,dimnames=list(year=2009:2011)))
>
> fbar(ple4)[,"2009"]
> ssb(ple4)[,"2009"]
> ssb(ple4)[,"2010"]
>
> Laurie
>
> On 27/10/14 10:36, Clara Ulrich wrote:
>> Hej, Thanks for help. I send my object - a stf from North Sea Haddock
>> with 10 iterations.
>>
>> Clara
>>
>>
>>
>> -----Original Message-----
>> From: flr-list-bounces at lists.r-forge.r-project.org
>> [mailto:flr-list-bounces at lists.r-forge.r-project.org] On Behalf Of laurie
>> Sent: 27 October 2014 09:47
>> To: flr-list at flr-project.org
>> Subject: Re: [FLR-list] ssb constraint with FLash
>>
>> Is it a bug or poor documentation?
>>
>> We used to have a page on TYFLR with all the different HCRs
>> implemented using FLash. This included the STECF ones with numerous
>> sequential constraints, on F, TAC, SSB etc. I have also implemented
>> some simpler interfaces for fwd. I am currently redoing this see
>> http://rscloud.iccat.int/Tutorials/MSE/hcr.pdf
>>
>> As well as being documentation this will also provide a set of tests
>> to make sure no bugs creep in during the winter.
>>
>> As Iago says could you provide an example, and if it is not already
>> included in hcr.pdf I will add it. After checking there isnt a bug of
>> course.
>>
>> Laurie
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 27/10/14 09:28, Iago MOSQUEIRA (JRC) wrote:
>>> Hi,
>>>
>>> I am trying to replicate the issue, using our dear ple4, but I failed
>>> to do so. If I set a min value for ssb in 2010, which is higher than
>>> what
>>> f=0.8 in 2009 would give me, I get as expected a lower F and the right
>>> ssb, try code below.
>>>
>>> Can you send me your FLStock object?
>>>
>>> Cheers,
>>>
>>>
>>> Iago
>>>
>>>
>>> library(FLash)
>>> library(FLAssess)
>>>
>>> data(ple4)
>>>
>>> ple4 <- stf(ple4,3)
>>>
>>> maxF <-fwdControl(data.frame(year=2009,val=0.8,quantity="f")) # an
>>> example with high F that decreases biomass a lot
>>>
>>> ple4 <-
>>> fwd(ple4,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residuals=
>>> FLQuant(3500000,dimnames=list(year=2009:2011)))
>>>
>>> fbar(ple4)[,"2009"]
>>>
>>> maxF <-fwdControl(data.frame(year=2009,val=c(0.8,NA),min=c(NA,350000),
>>> quantity=c("f","ssb")))
>>>
>>> ple4 <-
>>> fwd(ple4,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residuals=
>>> FLQuant(3500000,dimnames=list(year=2009:2011)))
>>>
>>> fbar(ple4)[,"2009"]
>>> ssb(ple4)[,"2009"]
>>> ssb(ple4)[,"2010"]
>>>
>>>
>>> On 25/10/14 21:35, Clara Ulrich wrote:
>>>> Hi all,
>>>>
>>>> We are just back from ICES MIXFISH, where we once again made much use
>>>> of FLash power... (still on R 2.15.3 windows 32 bits, we had some
>>>> troubles at the advice meeting in May with using the new FLFleet
>>>> package for R3.1, we haven't tried again - Flash 2.5.0)
>>>>
>>>> This time we wanted to some SSB-based HCR - Typically, we have a
>>>> target F with some SSB minimum constraints - for example the biomass
>>>> must stay above Bpa, or if the biomass is below Bpa, the target is
>>>> reduced such as SSB should be at least increasing...
>>>>
>>>> But I kept having troubles making it to work - I had tried this some
>>>> years ago and it worked OK as far as I remember, but last week I did
>>>> not manage to get around the problem.
>>>>
>>>> For example (with target F for 2014, and SSB constraint applying on
>>>> SSB at 1st January 2015 at the end of the fwd year)
>>>>
>>>> maxF <-fwdControl(data.frame(year=2014,val=0.8,quantity="f")) # an
>>>> example with high F that decreases biomass a lot Proj <-
>>>> fwd(MyObj,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residual
>>>> s=FLQuant(3500000,dimnames=list(year=2014:2015)))
>>>>
>>>> This works :
>>>> fbar(Proj)[,"2014"]
>>>> An object of class "FLQuant"
>>>> iters: 10
>>>> , , unit = unique, season = all, area = unique
>>>> year
>>>> age 2014
>>>> all 0.8(0)
>>>> units: f
>>>>
>>>> ssb(Proj)[,ac(2014:2015)]
>>>> An object of class "FLQuant"
>>>> iters: 10
>>>> , , unit = unique, season = all, area = unique
>>>> year
>>>> age 2014 2015
>>>> all 172983(0) 77323(0)
>>>> units: NA
>>>>
>>>> but this does not work (here an example where the SSB constraint
>>>> should be activated)
>>>>
>>>> maxF
>>>> <-fwdControl(data.frame(year=2014,val=c(0.8,NA),min=c(NA,150000),
>>>> quantity=c("f","ssb"))) Proj <-
>>>> fwd(MyObj,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residual
>>>> s=FLQuant(3500000,dimnames=list(year=2014:2015)))
>>>>
>>>> fbar(Proj)[,"2014"]
>>>> An object of class "FLQuant"
>>>> iters: 10
>>>> , , unit = unique, season = all, area = unique
>>>> year
>>>> age 2014
>>>> all 0.016914(0)
>>>> units: f
>>>>
>>>> ssb(Proj)[,ac(2014:2015)]
>>>> An object of class "FLQuant"
>>>> iters: 10
>>>> , , unit = unique, season = all, area = unique
>>>> year
>>>> age 2014 2015
>>>> all 172983(0) 172983(0)
>>>> units: NA
>>>>
>>>>
>>>> and this doesn't work either when the SSB is not constraining (e.g.
>>>> SSB limit so low that it is always achieved). Only if I specify ssb
>>>> as a value inn fwdControl does it compute correctly, but that is not
>>>> the idea, it should be a minimum
>>>>
>>>>
>>>> I have tried several ways around this but cannot find out... Any
>>>> idea of what is getting wrong?
>>>>
>>>> Thanks in advance,
>>>> Cheers
>>>> Clara
>>>> _______________________________________________
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>>>>
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--
Dr Iago Mosqueira
European Commission – Joint Research Center
Institute for the Protection and Security of the Citizen (IPSC)
Maritime Affairs Unit G04
TP 051, Via Enrico Fermi 2749
I-21027 Ispra (VA), Italy
Office : +39 0332 785413
Fax: +39 0332 789658
iago.mosqueira at jrc.ec.europa.eu
http://fishreg.jrc.ec.europa.eu/home
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