[FLR-list] ssb constraint with FLash
Clara Ulrich
clu at aqua.dtu.dk
Mon Oct 27 15:53:01 CET 2014
Hi Laurie,
In your example below, you use ssb as a target, not as a minimum. This was working also for me in the previous example, but that is not really what we want? F should be the target, but SSB is just a minimum threshold, exactly like a TAC constraint?
Clara
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 15:02
To: flr-list at lists.r-forge.r-project.org
Subject: Re: [FLR-list] ssb constraint with FLash
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> [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<mailto: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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