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<div class="moz-cite-prefix">Yes, we (Iago and me) were discussing
that issue. We shouldn't accept sparse data, the methods will have
to check each bin and deal with the missing observations. If we
force all lengths to be present we may loose a bit on space but
the methods wont need to check the length of the bins and workout
what is going on.<br>
<br>
Best<br>
<br>
EJ<br>
<br>
On 05/22/2013 04:18 PM, Laurie Kell wrote:<br>
</div>
<blockquote
cite="mid:CAAJ=99miuhS6+AevcmXo_sOanXa1JMWHT74nCXoX+kgNJ9MNuw@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>It could be due to sparse data and some size classes being
missing. For example going from a DB to a matrix.<br>
<br>
</div>
Laurie<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, May 22, 2013 at 4:05 PM,
Ernesto <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:ernesto.jardim@jrc.ec.europa.eu"
target="_blank">ernesto.jardim@jrc.ec.europa.eu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>Hi,<br>
<br>
That can be done already, the range name we use for age
is "max" and "min" so we can use it directly for
lengths.<br>
<br>
Not so sure about using different bin's size. Methods
would need to check each bin size ...<br>
<br>
One doubt, when using different bin's size aren't you
getting close to the age structure ? kind of slicing ?<br>
<br>
Best<br>
<br>
EJ
<div>
<div class="h5"><br>
<br>
On 05/22/2013 03:38 PM, Santiago Cerviño wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div>
<p class="MsoNormal"><font face="Arial"
color="navy"><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. </span></font></p>
<p class="MsoNormal"><font face="Arial"
color="navy"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font face="Arial"
color="navy"><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).</span></font></p>
<p class="MsoNormal"><font face="Arial"
color="navy"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font face="Arial"
color="navy"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">Santi</span></font></p>
<p class="MsoNormal"><font face="Arial"
color="navy"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"> </span></font></p>
<div style="border:none;border-left:solid blue
1.5pt;padding:0cm 0cm 0cm 4.0pt">
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<div>
<p class="MsoNormal"><font face="Times New
Roman" size="3" color="black"><span
style="font-size:12.0pt" lang="EN-GB"> </span></font></p>
</div>
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style="text-align:center" align="center"><font
face="Times New Roman" size="3"
color="black"><span
style="font-size:12.0pt;color:windowtext">
<hr size="2" width="100%" align="center">
</span></font></div>
<p class="MsoNormal"><b><font face="Tahoma"
color="black"><span
style="font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold">De:</span></font></b><font
face="Tahoma" color="black"><span
style="font-size:10.0pt;font-family:Tahoma;color:windowtext">
<a moz-do-not-send="true"
href="mailto:flr-list-bounces@lists.r-forge.r-project.org"
target="_blank">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"
target="_blank">mailto: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 moz-do-not-send="true"
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"></span></font></p>
</div>
<p class="MsoNormal"><font face="Times New
Roman" size="3" color="black"><span
style="font-size:12.0pt"> </span></font></p>
<div>
<p class="MsoNormal"><font face="Times New
Roman" size="3" color="black"><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:</span></font></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt"
type="cite">
<div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
face="Times New Roman" size="3"
color="black"><span
style="font-size:12.0pt">but wont
work with age slicing which is based
on > & <=. </span></font></p>
</div>
<p class="MsoNormal"><font face="Times New
Roman" size="3" color="black"><span
style="font-size:12.0pt">Laurie</span></font></p>
</div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
face="Times New Roman" size="3"
color="black"><span
style="font-size:12.0pt"> </span></font></p>
<div>
<p class="MsoNormal"><font face="Times New
Roman" size="3" color="black"><span
style="font-size:12.0pt">On Wed, May
22, 2013 at 2:41 PM, Ernesto <<a
moz-do-not-send="true"
href="mailto:ernesto.jardim@jrc.ec.europa.eu"
target="_blank">ernesto.jardim@jrc.ec.europa.eu</a>>
wrote:</span></font></p>
<div text="#000000" bgcolor="#FFFFFF">
<div>
<p class="MsoNormal"><font face="Times
New Roman" size="3" color="black"><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 </span></font></p>
<div>
<div>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt"><br>
<br>
On 05/22/2013 02:23 PM,
Laurie Kell wrote:</span></font></p>
</div>
</div>
</div>
<div>
<div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt"
type="cite">
<div>
<div>
<div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
face="Times New Roman"
size="3" color="black"><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.</span></font></p>
</div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
face="Times New Roman"
size="3" color="black"><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, ...?</span></font></p>
</div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
face="Times New Roman"
size="3" color="black"><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.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt">Otherwise
I can see a lot of time
being wasted in stock
assessments. well more
than normal.</span></font></p>
</div>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt">Laurie
</span></font></p>
</div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt"> </span></font></p>
<div>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt">On
Wed, May 22, 2013 at
1:07 PM, Ernesto <<a
moz-do-not-send="true"
href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank">ernesto.jardim@jrc.ec.europa.eu</a>>
wrote:</span></font></p>
<div>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt">On 05/22/2013 12:02 PM, Ernesto wrote:</span></font></p>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt">On 05/22/2013 11:34 AM, Sarah Kraak wrote:</span></font></p>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><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</span></font></p>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><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
moz-do-not-send="true" 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</span></font></p>
</div>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt">Hi,<br>
<br>
I've updated the readme
to reflect the latest
messages. </span></font></p>
<div>
<div>
<p class="MsoNormal"><font
face="Times New Roman"
size="3" color="black"><span
style="font-size:12.0pt"><br>
<br>
EJ<br>
<br>
-- <br>
Ernesto Jardim<<a
moz-do-not-send="true" 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
moz-do-not-send="true"
href="tel:%2B39%200332%20785311" value="+390332785311" target="_blank">+39
0332 785311</a><br>
Fax: <a
moz-do-not-send="true"
href="tel:%2B39%200332%20789658" value="+390332789658" target="_blank">+39
0332 789658</a><br>
<a
moz-do-not-send="true"
href="https://fishreg.jrc.ec.europa.eu/" target="_blank">https://fishreg.jrc.ec.europa.eu/</a><br>
<br>
<br>
_______________________________________________<br>
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<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">_______________________________________________</span></font></pre>
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<br>
</span></font></p>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">-- </span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">Ernesto Jardim<a moz-do-not-send="true" href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank"><ernesto.jardim@jrc.ec.europa.eu></a></span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">Fisheries Scientist</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">FISHREG – Scientific Support to Fisheries</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">IPSC Maritime Affairs Unit</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">EC Joint Research Center</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">TP 051, Via Enrico Fermi 2749</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">I-21027 Ispra (VA), Italy</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">Office : <a moz-do-not-send="true" href="tel:%2B39%200332%20785311" value="+390332785311" target="_blank">+39 0332 785311</a></span></font></pre>
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<br>
</span></font></p>
<fieldset></fieldset>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">_______________________________________________</span></font></pre>
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style="font-size:12.0pt"><br>
<br>
<br>
</span></font></p>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">-- </span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">Ernesto Jardim<a moz-do-not-send="true" href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank"><ernesto.jardim@jrc.ec.europa.eu></a></span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">Fisheries Scientist</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">FISHREG – Scientific Support to Fisheries</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">IPSC Maritime Affairs Unit</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">EC Joint Research Center</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">TP 051, Via Enrico Fermi 2749</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">I-21027 Ispra (VA), Italy</span></font></pre>
<pre><font face="Courier New" color="black"><span style="font-size:10.0pt">Office : <a moz-do-not-send="true" href="tel:%2B39%200332%20785311" value="+390332785311" target="_blank">+39 0332 785311</a></span></font></pre>
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</pre>
</blockquote>
<br>
<br>
<pre cols="72">--
Ernesto Jardim<a moz-do-not-send="true" href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank"><ernesto.jardim@jrc.ec.europa.eu></a>
Fisheries Scientist
FISHREG – Scientific Support to Fisheries
IPSC Maritime Affairs Unit
EC Joint Research Center
TP 051, Via Enrico Fermi 2749
I-21027 Ispra (VA), Italy
Office : <a moz-do-not-send="true" href="tel:%2B39%200332%20785311" value="+390332785311" target="_blank">+39 0332 785311</a>
Fax: <a moz-do-not-send="true" href="tel:%2B39%200332%20789658" value="+390332789658" target="_blank">+39 0332 789658</a>
<a moz-do-not-send="true" href="https://fishreg.jrc.ec.europa.eu/" target="_blank">https://fishreg.jrc.ec.europa.eu/</a>
</pre>
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<pre wrap="">_______________________________________________
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<pre class="moz-signature" cols="72">--
Ernesto Jardim<a class="moz-txt-link-rfc2396E" href="mailto:ernesto.jardim@jrc.ec.europa.eu"><ernesto.jardim@jrc.ec.europa.eu></a>
Fisheries Scientist
FISHREG – Scientific Support to Fisheries
IPSC Maritime Affairs Unit
EC Joint Research Center
TP 051, Via Enrico Fermi 2749
I-21027 Ispra (VA), Italy
Office : +39 0332 785311
Fax: +39 0332 789658
<a class="moz-txt-link-freetext" href="https://fishreg.jrc.ec.europa.eu/">https://fishreg.jrc.ec.europa.eu/</a>
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