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Thanks, but it is a bug that needs to be fixed. If the 1st age is 2
then you again get a different result!<br>
<br>
Laurie<br>
<br>
<div class="moz-cite-prefix">On 26/02/16 17:24, Simon Fischer
(Cefas) wrote:<br>
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<p class="MsoNormal"><span style="color:#1F497D">Hi Laurie,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thank you very
much for your solution, works perfectly!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Simon<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
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1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="color:windowtext;mso-fareast-language:EN-GB"
lang="EN-US">From:</span></b><span
style="color:windowtext;mso-fareast-language:EN-GB"
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> 26 February 2016 15:32<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] fwd(), catch differs from
targeted catch<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span
style="font-size:10.0pt;font-family:"Courier
New",serif"><br>
</span>There is a problem with indexing ages, if the ages go
from 1, then it is OK<br>
<br>
<tt><span style="font-size:10.0pt">load("/home/laurie/Desktop/temp/data.RData")</span></tt><span
style="font-size:10.0pt;font-family:"Courier
New",serif"><br>
<tt>ctrl <- fwdControl(data.frame(year = 0, quantity =
"catch", val = 111111111))</tt><br>
<tt>stock=stock[-1]</tt><br>
<tt>res <- fwd(stock, ctrl = ctrl, sr = srr)</tt><br>
<tt>catch(res)[,"0"]</tt><br>
<br>
</span>i.e. any 1st age other than 1 causes a problem. <br>
<br>
Laurie<br>
<br>
<span style="font-size:12.0pt;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<div>
<p class="MsoNormal">On 26/02/16 13:25, Simon Fischer (Cefas)
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I am working on mse simulations with
hypothetical stocks. The stocks are created from life
history parameters which are fished at 2Fmsy until an
equilibrium is reached. This state is then used as starting
point for the simulations.<o:p></o:p></p>
<p class="MsoNormal">I use fwd() to project the stock
(FLStock) and use catch as a target. Somehow, for some
stocks the catch predicted by fwd() differs considerably
from the targeted catch (the actual catch is higher than the
targeted catch).<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Did anyone else encounter this behaviour
or knows how to avoid it?<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I use the current versions of R and FLR.
Attached to this email is a minimum reproducible example
that shows this behaviour, the stock object and my
sessionInfo().<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thanks in advance,<o:p></o:p></p>
<p class="MsoNormal">Simon<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Minimal reproducible example:<o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### load FLR</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">library(FLash)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">library(FLAssess)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### load data </span>
<o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">load("data.RData")</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### contains FLStock "stock" and FLSR
"srr"</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### extend stock for 1 year</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">stock <- stf(object = stock, nyears =
1)
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### create fwdControl object</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">ctrl <- fwdControl(data.frame(year =
1, quantity = "catch", val = 111697431))</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### fwd prediction</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">res <- fwd(stock, ctrl = ctrl, sr =
srr)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### check predicted catch</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">catch(res)[,ac(1)]</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">### 115308236 and NOT 111697431 as
specified in the control object?</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#> sessionInfo()</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#R version 3.2.3 (2015-12-10)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#Platform: i386-w64-mingw32/i386 (32-bit)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#Running under: Windows 7 x64 (build
7601) Service Pack 1</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#locale:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[1] LC_COLLATE=English_United
Kingdom.1252
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[2] LC_CTYPE=English_United
Kingdom.1252
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[3] LC_MONETARY=English_United
Kingdom.1252</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[4]
LC_NUMERIC=C
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[5] LC_TIME=English_United
Kingdom.1252
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#attached base packages:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[1] stats graphics grDevices
utils datasets methods base
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#other attached packages:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[1] FLAssess_2.5.20130716
FLash_2.5.2 FLCore_2.5.20160107
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[4] Matrix_1.2-3
MASS_7.3-45 lattice_0.20-33
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#loaded via a namespace (and not
attached):</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier
New",serif">#[1] grid_3.2.3 stats4_3.2.3</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif;mso-fareast-language:EN-GB"><br>
<br>
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