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I know that, I was just checking that the algorithm that estimated
SSB was working.<br>
The final result is also a check for the values that the fwdControl
with val and min should get.<br>
<br>
<div class="moz-cite-prefix">On 27/10/14 15:53, Clara Ulrich wrote:<br>
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi
Laurie,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Clara<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"
lang="EN-US">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"
lang="EN-US">
<a class="moz-txt-link-abbreviated" href="mailto:flr-list-bounces@lists.r-forge.r-project.org">flr-list-bounces@lists.r-forge.r-project.org</a>
[<a class="moz-txt-link-freetext" href="mailto:flr-list-bounces@lists.r-forge.r-project.org">mailto:flr-list-bounces@lists.r-forge.r-project.org</a>] <b>On
Behalf Of </b>laurie<br>
<b>Sent:</b> 27 October 2014 15:02<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:flr-list@lists.r-forge.r-project.org">flr-list@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> Re: [FLR-list] ssb constraint with FLash<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">There are a
couple of issues neither of which should cause a problem but
may point to a bug somewhere.
<br>
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.
<br>
It looks like there is a bug in "[" i.e.<br>
<br>
<tt><span style="font-size:10.0pt">range(ple4[-1])</span></tt><span
style="font-size:10.0pt;font-family:"Courier New""><br>
<tt> min max plusgroup minyear maxyear
minfbar maxfbar </tt><br>
<tt> 2 10 -1 1957
2008 2 6 </tt><br>
<br>
<br>
</span>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.<br>
<br>
<span style="font-size:10.0pt;font-family:"Courier
New""><br>
<tt>plot(window(stk,start=2006))</tt><br>
<br>
<tt>stk=window(iter(MyObj,1),end=2008)</tt><br>
<tt>stk =fwdWindow(stk,eql,end=2010)</tt><br>
<br>
<tt>target <-fwdControl(data.frame(year =c(2009,2009),</tt><br>
<tt> val =c(.3,180000),</tt><br>
<tt> #min =c(NA,180000),</tt><br>
<tt> quantity=c("f","ssb")))</tt><br>
<br>
<tt>stk.=fwd(stk,ctrl=target ,</tt><br>
<tt> sr=eql)</tt><br>
</span><br>
<tt><span style="font-size:10.0pt">fbar(stk.)[,ac(2009)]</span></tt><span
style="font-size:10.0pt;font-family:"Courier New""><br>
<tt>An object of class "FLQuant"</tt><br>
<tt>, , unit = unique, season = all, area = unique</tt><br>
<br>
<tt> year</tt><br>
<tt>age 2009 </tt><br>
<tt> all 0.21768</tt><br>
<br>
<tt>units: f </tt><br>
<tt>> ssb( stk.)[,ac(2009:2010)]</tt><br>
<tt>An object of class "FLQuant"</tt><br>
<tt>, , unit = unique, season = all, area = unique</tt><br>
<br>
<tt> year</tt><br>
<tt>age 2009 2010 </tt><br>
<tt> all 227124 180000</tt><br>
<br>
<tt>units: NA </tt><br>
<br>
<br>
</span>Note that the SSS constraint refers to the SSB at the
end of the year if harvest.spwn.<br>
<span style="font-size:10.0pt;font-family:"Courier
New""><br>
</span>Laurie<o:p></o:p></p>
<div>
<p class="MsoNormal">On 27/10/14 10:36, Clara Ulrich wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Hej, Thanks for help. I send my object - a stf from North Sea Haddock with 10 iterations.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Clara<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: <a moz-do-not-send="true" href="mailto:flr-list-bounces@lists.r-forge.r-project.org">flr-list-bounces@lists.r-forge.r-project.org</a> [<a moz-do-not-send="true" href="mailto:flr-list-bounces@lists.r-forge.r-project.org">mailto:flr-list-bounces@lists.r-forge.r-project.org</a>] On Behalf Of laurie<o:p></o:p></pre>
<pre>Sent: 27 October 2014 09:47<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true" href="mailto:flr-list@flr-project.org">flr-list@flr-project.org</a><o:p></o:p></pre>
<pre>Subject: Re: [FLR-list] ssb constraint with FLash<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Is it a bug or poor documentation?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>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 <a moz-do-not-send="true" href="http://rscloud.iccat.int/Tutorials/MSE/hcr.pdf">http://rscloud.iccat.int/Tutorials/MSE/hcr.pdf</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>As well as being documentation this will also provide a set of tests to make sure no bugs creep in during the winter.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>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.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Laurie<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>On 27/10/14 09:28, Iago MOSQUEIRA (JRC) wrote:<o:p></o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Hi,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I am trying to replicate the issue, using our dear ple4, but I failed <o:p></o:p></pre>
<pre>to do so. If I set a min value for ssb in 2010, which is higher than <o:p></o:p></pre>
<pre>what<o:p></o:p></pre>
<pre>f=0.8 in 2009 would give me, I get as expected a lower F and the right <o:p></o:p></pre>
<pre>ssb, try code below.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Can you send me your FLStock object?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Iago<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>library(FLash)<o:p></o:p></pre>
<pre>library(FLAssess)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>data(ple4)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>ple4 <- stf(ple4,3)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>maxF <-fwdControl(data.frame(year=2009,val=0.8,quantity="f")) # an <o:p></o:p></pre>
<pre>example with high F that decreases biomass a lot<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>ple4 <-<o:p></o:p></pre>
<pre>fwd(ple4,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residuals=<o:p></o:p></pre>
<pre>FLQuant(3500000,dimnames=list(year=2009:2011)))<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>fbar(ple4)[,"2009"]<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>maxF <-fwdControl(data.frame(year=2009,val=c(0.8,NA),min=c(NA,350000),<o:p></o:p></pre>
<pre>quantity=c("f","ssb")))<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>ple4 <-<o:p></o:p></pre>
<pre>fwd(ple4,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residuals=<o:p></o:p></pre>
<pre>FLQuant(3500000,dimnames=list(year=2009:2011)))<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>fbar(ple4)[,"2009"]<o:p></o:p></pre>
<pre>ssb(ple4)[,"2009"]<o:p></o:p></pre>
<pre>ssb(ple4)[,"2010"]<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>On 25/10/14 21:35, Clara Ulrich wrote:<o:p></o:p></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Hi all,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>We are just back from ICES MIXFISH, where we once again made much use <o:p></o:p></pre>
<pre>of FLash power... (still on R 2.15.3 windows 32 bits, we had some <o:p></o:p></pre>
<pre>troubles at the advice meeting in May with using the new FLFleet <o:p></o:p></pre>
<pre>package for R3.1, we haven't tried again - Flash 2.5.0)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>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...<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>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.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>For example (with target F for 2014, and SSB constraint applying on <o:p></o:p></pre>
<pre>SSB at 1st January 2015 at the end of the fwd year)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>maxF <-fwdControl(data.frame(year=2014,val=0.8,quantity="f")) # an <o:p></o:p></pre>
<pre>example with high F that decreases biomass a lot Proj <- <o:p></o:p></pre>
<pre>fwd(MyObj,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residual<o:p></o:p></pre>
<pre>s=FLQuant(3500000,dimnames=list(year=2014:2015)))<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>This works :<o:p></o:p></pre>
<pre>fbar(Proj)[,"2014"]<o:p></o:p></pre>
<pre> An object of class "FLQuant"<o:p></o:p></pre>
<pre> iters: 10<o:p></o:p></pre>
<pre> , , unit = unique, season = all, area = unique<o:p></o:p></pre>
<pre> year<o:p></o:p></pre>
<pre> age 2014<o:p></o:p></pre>
<pre> all 0.8(0) <o:p></o:p></pre>
<pre> units: f<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>ssb(Proj)[,ac(2014:2015)]<o:p></o:p></pre>
<pre> An object of class "FLQuant"<o:p></o:p></pre>
<pre> iters: 10<o:p></o:p></pre>
<pre> , , unit = unique, season = all, area = unique<o:p></o:p></pre>
<pre> year<o:p></o:p></pre>
<pre> age 2014 2015<o:p></o:p></pre>
<pre> all 172983(0) 77323(0)<o:p></o:p></pre>
<pre> units: NA<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>but this does not work (here an example where the SSB constraint <o:p></o:p></pre>
<pre>should be activated)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>maxF <o:p></o:p></pre>
<pre><-fwdControl(data.frame(year=2014,val=c(0.8,NA),min=c(NA,150000), <o:p></o:p></pre>
<pre>quantity=c("f","ssb"))) Proj <- <o:p></o:p></pre>
<pre>fwd(MyObj,ctrl=maxF,sr=list(model="mean",params=FLPar(1)),sr.residual<o:p></o:p></pre>
<pre>s=FLQuant(3500000,dimnames=list(year=2014:2015)))<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>fbar(Proj)[,"2014"]<o:p></o:p></pre>
<pre> An object of class "FLQuant"<o:p></o:p></pre>
<pre> iters: 10<o:p></o:p></pre>
<pre> , , unit = unique, season = all, area = unique<o:p></o:p></pre>
<pre> year<o:p></o:p></pre>
<pre> age 2014<o:p></o:p></pre>
<pre> all 0.016914(0) <o:p></o:p></pre>
<pre> units: f<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>ssb(Proj)[,ac(2014:2015)]<o:p></o:p></pre>
<pre> An object of class "FLQuant"<o:p></o:p></pre>
<pre> iters: 10<o:p></o:p></pre>
<pre> , , unit = unique, season = all, area = unique<o:p></o:p></pre>
<pre> year<o:p></o:p></pre>
<pre> age 2014 2015<o:p></o:p></pre>
<pre> all 172983(0) 172983(0)<o:p></o:p></pre>
<pre> units: NA<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>and this doesn't work either when the SSB is not constraining (e.g. <o:p></o:p></pre>
<pre>SSB limit so low that it is always achieved). Only if I specify ssb <o:p></o:p></pre>
<pre>as a value inn fwdControl does it compute correctly, but that is not <o:p></o:p></pre>
<pre>the idea, it should be a minimum<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I have tried several ways around this but cannot find out... Any idea of what is getting wrong?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Thanks in advance,<o:p></o:p></pre>
<pre>Cheers<o:p></o:p></pre>
<pre>Clara<o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
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