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<div class="moz-cite-prefix">I have modified DESCRIPTION etc so that
it compiles, as we are using it for our albacore assessment this
week. Mainly the io routines for MFCL and SS.<br>
<br>
Laurie<br>
<br>
On 17/06/13 09:44, Ernesto Jardim wrote:<br>
</div>
<blockquote
cite="mid:CAC03QWAdd-D-guQGdVQKvo1wVku77reKZvr+4exT-g5MFD=Gzw@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>Yes, sure. I will finish our things this week and post it
as well. Not sure it will work without the a4a pkg though
...<br>
<br>
</div>
Best<br>
<br>
</div>
EJ<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
On Fri, May 24, 2013 at 9:11 AM, Laurie Kell <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:lauriekell@googlemail.com" target="_blank">lauriekell@googlemail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>
<div>
<div>
<div>I have some simple functions, e.g. the
powell-wetherall method, calculation of moments,
... <br>
</div>
A class that implements the "Survival Estimation in
Non-Equilibrium situations" method. These all work
on FLQuant and FLPar objects.<br>
</div>
I propose to add these to <a moz-do-not-send="true"
href="https://github.com/ejardim/FLMethLen.git"
target="_blank">https://github.com/ejardim/FLMethLen.git</a><br>
<br>
</div>
I also have methods that get length/age data from SS and
Multifan-Cl, these could go there as well.<br>
</div>
<div>Would this be OK?<br>
</div>
<div><br>
</div>
Laurie<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, May 22, 2013 at 4:25 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>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
<div>
<div><br>
<br>
On 05/22/2013 04:18 PM, Laurie Kell wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote 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><br>
<br>
On 05/22/2013 03:38 PM, Santiago
Cerviño wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div>
<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. </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"> </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).</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"> </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</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"> </span></font></p>
<div
style="border:none;border-left:solid
blue 1.5pt;padding:0cm 0cm
0cm 4.0pt">
<div>
<div>
<p class="MsoNormal"><font
size="3"
color="black"
face="Times New
Roman"><span
style="font-size:12.0pt"
lang="EN-GB"> </span></font></p>
</div>
<div class="MsoNormal"
style="text-align:center"
align="center"><font
size="3" color="black"
face="Times New Roman"><span
style="font-size:12.0pt;color:windowtext">
<hr size="2"
width="100%"
align="center"> </span></font></div>
<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
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
size="3" color="black"
face="Times New Roman"><span
style="font-size:12.0pt"> </span></font></p>
<div>
<p class="MsoNormal"><font
size="3" color="black"
face="Times New Roman"><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
size="3"
color="black"
face="Times New
Roman"><span
style="font-size:12.0pt">but
wont work with
age slicing
which is based
on > &
<=. </span></font></p>
</div>
<p class="MsoNormal"><font
size="3"
color="black"
face="Times New
Roman"><span
style="font-size:12.0pt">Laurie</span></font></p>
</div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
size="3"
color="black"
face="Times New
Roman"><span
style="font-size:12.0pt"> </span></font></p>
<div>
<p class="MsoNormal"><font
size="3"
color="black"
face="Times New
Roman"><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
size="3"
color="black"
face="Times
New Roman"><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
size="3"
color="black"
face="Times
New Roman"><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 size="3" color="black" face="Times
New Roman"><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 size="3" color="black" face="Times
New Roman"><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 size="3" color="black" face="Times
New Roman"><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
size="3"
color="black"
face="Times
New Roman"><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
size="3"
color="black"
face="Times
New Roman"><span
style="font-size:12.0pt">Laurie </span></font></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-bottom:12.0pt"><font size="3" color="black" face="Times
New Roman"><span
style="font-size:12.0pt"> </span></font></p>
<div>
<p
class="MsoNormal"><font
size="3"
color="black"
face="Times
New Roman"><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
size="3"
color="black"
face="Times
New Roman"><span
style="font-size:12.0pt">On 05/22/2013 12:02 PM, Ernesto wrote:</span></font></p>
<p
class="MsoNormal"><font
size="3"
color="black"
face="Times
New Roman"><span
style="font-size:12.0pt">On 05/22/2013 11:34 AM, Sarah Kraak wrote:</span></font></p>
<p
class="MsoNormal"><font
size="3"
color="black"
face="Times
New Roman"><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
size="3"
color="black"
face="Times
New Roman"><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
size="3"
color="black"
face="Times
New Roman"><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
size="3"
color="black"
face="Times
New Roman"><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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mailing list<br>
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</div>
<p
class="MsoNormal"><font
size="3"
color="black"
face="Times
New Roman"><span
style="font-size:12.0pt"><br>
<br>
</span></font></p>
<fieldset></fieldset>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">_______________________________________________</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">flr-list mailing list</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><a moz-do-not-send="true" href="mailto:flr-list@flr-project.org" target="_blank">flr-list@flr-project.org</a></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><a moz-do-not-send="true" href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list</a></span></font></pre>
</blockquote>
<p
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face="Times
New Roman"><span
style="font-size:12.0pt"><br>
<br>
<br>
</span></font></p>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">-- </span></font></pre>
<pre><font color="black" face="Courier New"><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 color="black" face="Courier New"><span style="font-size:10.0pt">Fisheries Scientist</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">FISHREG – Scientific Support to Fisheries</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">IPSC Maritime Affairs Unit</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">EC Joint Research Center</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">TP 051, Via Enrico Fermi 2749</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">I-21027 Ispra (VA), Italy</span></font></pre>
<pre><font color="black" face="Courier New"><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>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Fax: <a moz-do-not-send="true" href="tel:%2B39%200332%20789658" value="+390332789658" target="_blank">+39 0332 789658</a></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><a moz-do-not-send="true" href="https://fishreg.jrc.ec.europa.eu/" target="_blank">https://fishreg.jrc.ec.europa.eu/</a></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre>
</div>
</div>
</div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
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color="black"
face="Times New
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style="font-size:12.0pt"><br>
_______________________________________________<br>
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<p class="MsoNormal"><font
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face="Times New Roman"><span
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<br>
<br>
</span></font></p>
<fieldset></fieldset>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">_______________________________________________</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">flr-list mailing list</span></font></pre>
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<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><a moz-do-not-send="true" href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/flr-list</a></span></font></pre>
</blockquote>
<p class="MsoNormal"><font
size="3" color="black"
face="Times New Roman"><span
style="font-size:12.0pt"><br>
<br>
<br>
</span></font></p>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">-- </span></font></pre>
<pre><font color="black" face="Courier New"><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 color="black" face="Courier New"><span style="font-size:10.0pt">Fisheries Scientist</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">FISHREG – Scientific Support to Fisheries</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">IPSC Maritime Affairs Unit</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">EC Joint Research Center</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">TP 051, Via Enrico Fermi 2749</span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">I-21027 Ispra (VA), Italy</span></font></pre>
<pre><font color="black" face="Courier New"><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>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt">Fax: <a moz-do-not-send="true" href="tel:%2B39%200332%20789658" value="+390332789658" target="_blank">+39 0332 789658</a></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"><a moz-do-not-send="true" href="https://fishreg.jrc.ec.europa.eu/" target="_blank">https://fishreg.jrc.ec.europa.eu/</a></span></font></pre>
<pre><font color="black" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre>
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</blockquote>
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<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>
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</blockquote>
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<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>
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<pre wrap="">_______________________________________________
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