[FLR-list] ssb constraint with FLash
laurie
lauriekell at gmail.com
Mon Oct 27 15:01:40 CET 2014
There are a couple of issues neither of which should cause a problem but
may point to a bug somewhere.
The ple4 object differs from the one Clara is using as it start at age 0
not age 1, plus it doesnt come from XSA so the F in the plusgroup is not
the same as in plusgrpoup-1.
It looks like there is a bug in "[" i.e.
range(ple4[-1])
min max plusgroup minyear maxyear minfbar maxfbar
2 10 -1 1957 2008 2 6
The following code works as expected, it is a long winded way of
constraining SSB. It points in a problem not in the estimation procedure
(LU decomposition) but maybe how it is being set up.
plot(window(stk,start=2006))
stk=window(iter(MyObj,1),end=2008)
stk =fwdWindow(stk,eql,end=2010)
target <-fwdControl(data.frame(year =c(2009,2009),
val =c(.3,180000),
#min =c(NA,180000),
quantity=c("f","ssb")))
stk.=fwd(stk,ctrl=target ,
sr=eql)
fbar(stk.)[,ac(2009)]
An object of class "FLQuant"
, , unit = unique, season = all, area = unique
year
age 2009
all 0.21768
units: f
> ssb( stk.)[,ac(2009:2010)]
An object of class "FLQuant"
, , unit = unique, season = all, area = unique
year
age 2009 2010
all 227124 180000
units: NA
Note that the SSS constraint refers to the SSB at the end of the year if
harvest.spwn.
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
>>> _______________________________________________
>>> flr-list mailing list
>>> flr-list at flr-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list
>>>
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