<div dir="ltr"><div>Think we need to define the default behaviour and then be explicit about any exceptions in particular cases. Good that we are having this discussion 1st <br><br></div><div>Laurie<br></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Wed, May 22, 2013 at 3:38 PM, Santiago Cerviño <span dir="ltr"><<a href="mailto:santiago.cervino@vi.ieo.es" target="_blank">santiago.cervino@vi.ieo.es</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy" lang="EN-GB">Length based models
usually group length classes for different causes. Sometimes you do not have
the whole information; sometimes you need to simplify your model; you might need
to make big groups for larger fish and small ones for medium size fish, etc. I
think len bins should be user defined without constraints. It is also important
to have the whole information (lower length and upper length) for each bin somewhere.
This information will be needed. <u></u><u></u></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy" lang="EN-GB"><u></u> <u></u></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy" lang="EN-GB">Could work this idea that
keeps consistency with FLR age names using only one number? For instance 5, 12,
20, 30 that means 5-12, 12-20, 20-30, 30-??. We would only need that maximum length
is defined somewhere to know the size of the last bin (minage, maxage slots
used for minlen maxlen).<u></u><u></u></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy" lang="EN-GB"><u></u> <u></u></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy" lang="EN-GB">Santi<u></u><u></u></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy" lang="EN-GB"><u></u> <u></u></span></font></p>
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<p class="MsoNormal"><b><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold">De:</span></font></b><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma;color:windowtext"> <a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a>
[mailto:<a href="mailto:flr-list-bounces@lists.r-forge.r-project.org" target="_blank">flr-list-bounces@lists.r-forge.r-project.org</a>] <b><span style="font-weight:bold">En nombre de </span></b>Ernesto<br>
<b><span style="font-weight:bold">Enviado el:</span></b> 22 May 2013 13:55<br>
<b><span style="font-weight:bold">Para:</span></b>
<a href="mailto:flr-list@r-forge.wu-wien.ac.at" target="_blank">flr-list@r-forge.wu-wien.ac.at</a><br>
<b><span style="font-weight:bold">Asunto:</span></b> Re: [FLR-list] size</span></font><font color="black"><span style="color:windowtext"><u></u><u></u></span></font></p>
</div><div><div class="h5">
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><u></u> <u></u></span></font></p>
<div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">It won't work in several situations and IMO trying to
find a solution for all doesn't work. We need to find a solution that works and
implement methods for the others. We may try to be consistent with
"age" and use [10,11) represented by "10" in the length
names.<br>
<br>
Best<br>
<br>
EJ<br>
<br>
On 05/22/2013 02:43 PM, Laurie Kell wrote:<u></u><u></u></span></font></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt" type="cite">
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<p class="MsoNormal" style="margin-bottom:12.0pt"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">but wont work with age
slicing which is based on > & <=. <u></u><u></u></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">Laurie<u></u><u></u></span></font></p>
</div>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><u></u> <u></u></span></font></p>
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<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">On Wed, May 22, 2013 at 2:41 PM, Ernesto <<a href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank">ernesto.jardim@jrc.ec.europa.eu</a>> wrote:<u></u><u></u></span></font></p>
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<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">Hi,<br>
<br>
Yes, that is a problem that we need to sort out. I'm considering using
midpoints. It has the advantage of being easy to coerce into numeric. In most
cases that's what one needs for computations. Using boundaries will require
other(s) operation(s) to get midpoints.<br>
<br>
Best<br>
<br>
EJ <u></u><u></u></span></font></p>
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<div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><br>
<br>
On 05/22/2013 02:23 PM, Laurie Kell wrote:<u></u><u></u></span></font></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt" type="cite">
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<p class="MsoNormal" style="margin-bottom:12.0pt"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">There is an issue, boring
but may be important to agree on now, i.e. labeling of length bins.<u></u><u></u></span></font></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">What does a length bin
mean, i.e. if the "quant" dim represents length? and the values are
5, 10, ...?<u></u><u></u></span></font></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">In the mixdist package
these are the righthand boundaries i.e. they represent (0,5] and (5,10]. But if
they are the lefthand boundaries then they represent (5,10] and (10,INF]. Or
they could be midpoints. One option would be to explicitly label the bins with
the boundaries and then have methods for going backwards and forwards between
parametric and non-parametric methods. Or to have an attribute that tracks the
properties.<u></u><u></u></span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">Otherwise I can see a lot of time being wasted in
stock assessments. well more than normal.<u></u><u></u></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">Laurie <u></u><u></u></span></font></p>
</div>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><u></u> <u></u></span></font></p>
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<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">On Wed, May 22, 2013 at 1:07 PM, Ernesto <<a href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank">ernesto.jardim@jrc.ec.europa.eu</a>> wrote:<u></u><u></u></span></font></p>
<div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">On 05/22/2013 12:02 PM, Ernesto wrote:<u></u><u></u></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">On 05/22/2013 11:34 AM, Sarah Kraak wrote:<u></u><u></u></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">Hi FLR-guys,<br>
<br>
As you know I am not an active FLR user, but last year I showed some interest
in whether you have size-based stuff in FLR (see attached email). In the
meanwhile Coilin Minto and myself have been working on something (also attached
- note this is a draft of the idea; at the moment we are working on the code to
get the final graphs out) which we are coding in R but which could/should
eventually been done in FLR. Perhaps you are interested.<br>
<br>
Cheers,<br>
Sarah<u></u><u></u></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><br>
Hi,<br>
<br>
Following Laurie's suggestion I've started a git repository for length<br>
methods in FLRhttps://<a href="http://github.com/ejardim/FLMethLen" target="_blank">github.com/ejardim/FLMethLen</a><br>
<br>
Maybe our first task should be o write down what we're doing with length<br>
data. Laurie's working on ALKs, so I guess you're interested in<br>
converting length frequencies to ages for stock assessment !? We (a4a)<br>
are working on OMs and how to generate them from length based data so<br>
that uncertainty on the growth model can be included in the MSE. Sarah<br>
and Colin Minto are working on selectivity. What else ?<br>
<br>
Best<br>
<br>
EJ<u></u><u></u></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt">Hi,<br>
<br>
I've updated the readme to reflect the latest messages. <u></u><u></u></span></font></p>
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<div>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><br>
<br>
EJ<br>
<br>
-- <br>
Ernesto Jardim<<a href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank">ernesto.jardim@jrc.ec.europa.eu</a>><br>
Fisheries Scientist<br>
FISHREG – Scientific Support to Fisheries<br>
IPSC Maritime Affairs Unit<br>
EC Joint Research Center<br>
TP 051, Via Enrico Fermi 2749<br>
I-21027 Ispra (VA), Italy<br>
Office : <a href="tel:%2B39%200332%20785311" value="+390332785311" target="_blank">+39 0332 785311</a><br>
Fax: <a href="tel:%2B39%200332%20789658" value="+390332789658" target="_blank">+39 0332 789658</a><br>
<a href="https://fishreg.jrc.ec.europa.eu/" target="_blank">https://fishreg.jrc.ec.europa.eu/</a><br>
<br>
<br>
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</div>
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<br>
<u></u><u></u></span></font></p>
<fieldset></fieldset><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">_______________________________________________<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">flr-list mailing list<u></u><u></u></span></font></pre>
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</blockquote>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><br>
<br>
<br>
<u></u><u></u></span></font></p>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">-- <u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Ernesto Jardim<a href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank"><ernesto.jardim@jrc.ec.europa.eu></a><u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Fisheries Scientist<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">FISHREG – Scientific Support to Fisheries<u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">IPSC Maritime Affairs Unit<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">EC Joint Research Center<u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">TP 051, Via Enrico Fermi 2749<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">I-21027 Ispra (VA), Italy<u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Office : <a href="tel:%2B39%200332%20785311" value="+390332785311" target="_blank">+39 0332 785311</a><u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Fax: <a href="tel:%2B39%200332%20789658" value="+390332789658" target="_blank">+39 0332 789658</a><u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><a href="https://fishreg.jrc.ec.europa.eu/" target="_blank">https://fishreg.jrc.ec.europa.eu/</a><u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><u></u> <u></u></span></font></pre>
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<br>
<br>
</span></font></p><fieldset></fieldset><font color="black" face="Times New Roman" size="3"><u></u><u></u></font><p></p>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">_______________________________________________<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">flr-list mailing list<u></u><u></u></span></font></pre>
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</blockquote>
<p class="MsoNormal"><font color="black" face="Times New Roman" size="3"><span style="font-size:12.0pt"><br>
<br>
<br>
<u></u><u></u></span></font></p>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">-- <u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Ernesto Jardim<a href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank"><ernesto.jardim@jrc.ec.europa.eu></a><u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Fisheries Scientist<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">FISHREG – Scientific Support to Fisheries<u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">IPSC Maritime Affairs Unit<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">EC Joint Research Center<u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">TP 051, Via Enrico Fermi 2749<u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">I-21027 Ispra (VA), Italy<u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Office : <a href="tel:%2B39%200332%20785311" value="+390332785311" target="_blank">+39 0332 785311</a><u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Fax: <a href="tel:%2B39%200332%20789658" value="+390332789658" target="_blank">+39 0332 789658</a><u></u><u></u></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><a href="https://fishreg.jrc.ec.europa.eu/" target="_blank">https://fishreg.jrc.ec.europa.eu/</a><u></u><u></u></span></font></pre><pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><u></u> <u></u></span></font></pre>
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