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<font size="+1"><tt>Dear all,<br>
<br>
</tt><tt>We're happy to announce that FLa4a is now in version
1.0.0 ! A milestone in every software project.</tt><tt><br>
</tt><tt><br>
FLa4a, is an R package which implements the a4a stock assessment
framework and the methods to model M and growth (see intro here
<a class="moz-txt-link-freetext"
href="http://www.flr-project.org/FLa4a/articles/introduction.pdf">http://www.flr-project.org/FLa4a/articles/introduction.pdf</a>).
It's based on FLR and ADMB. The first for data structures and
supporting methods and the second for fitting stock assessment
models. <br>
<br>
The package is released under the open source license EUPL 1.1 (<a
class="moz-txt-link-freetext"
href="http://ec.europa.eu/idabc/servlets/Doc027f.pdf?id=31096"><a class="moz-txt-link-freetext" href="http://ec.europa.eu/idabc/servlets/Doc027f.pdf?id=31096">http://ec.europa.eu/idabc/servlets/Doc027f.pdf?id=31096</a></a>).
</tt></font><font size="+1"><tt><font size="+1"><tt>All the code
is available in github (<a class="moz-txt-link-freetext"
href="https://github.com/flr/FLa4a">https://github.com/flr/FLa4a</a>).</tt></font>
</tt></font><font size="+1"><tt><font size="+1"><tt>There's also a
new webpage (<a class="moz-txt-link-freetext"
href="http://www.flr-project.org/FLa4a/">http://www.flr-project.org/FLa4a/</a>)
where you'll find the package and all the documentation. <br>
</tt><tt><br>
</tt></font></tt></font><font size="+1"><tt><font size="+1"><tt>FLa4a
runs on R versions above 3.1. To install the package open
your R session and type:</tt><tt><br>
</tt><tt><br>
install.packages(c(“copula”,“triangle”, “coda”))</tt><tt><br>
</tt><code class="sourceCode r"><span class="kw">install.packages</span>(c(<span
class="st">"FLa4a","FLCore")</span>, <span class="dt">repos=</span><span
class="st"><a class="moz-txt-link-rfc2396E"
href="http://flr-project.org/R">"http://flr-project.org/R"</a></span>)</code><tt><br>
</tt><tt> </tt></font><br>
The most important addition to version 1.0.0 was documentation.
There's now a full set of man pages, reached through the common
'?' method, and a set of vignettes:</tt><tt><br>
</tt><tt>- Introduction to FLa4a (</tt></font><font size="+1"><tt><font
size="+1"><tt><a class="moz-txt-link-freetext"
href="http://www.flr-project.org/FLa4a/articles/introduction.pdf">http://www.flr-project.org/FLa4a/articles/introduction.pdf</a>)</tt></font></tt><tt><br>
</tt><tt>- Natural Mortality Modelling (<a
class="moz-txt-link-freetext"
href="http://www.flr-project.org/FLa4a/articles/M.pdf"><a class="moz-txt-link-freetext" href="http://www.flr-project.org/FLa4a/articles/M.pdf">http://www.flr-project.org/FLa4a/articles/M.pdf</a></a>)</tt><tt><br>
</tt><tt>- Modelling Individual Growth and Using Stochastic
Slicing to Convert Length-based Data Into Age-based Data (<a
class="moz-txt-link-freetext"
href="http://www.flr-project.org/FLa4a/articles/growth.pdf"><a class="moz-txt-link-freetext" href="http://www.flr-project.org/FLa4a/articles/growth.pdf">http://www.flr-project.org/FLa4a/articles/growth.pdf</a></a>)</tt><tt><br>
</tt><tt>- The a4a Stock Assessment Modelling Framework (<a
class="moz-txt-link-freetext"
href="http://www.flr-project.org/FLa4a/articles/sca.pdf"><a class="moz-txt-link-freetext" href="http://www.flr-project.org/FLa4a/articles/sca.pdf">http://www.flr-project.org/FLa4a/articles/sca.pdf</a></a>)</tt><tt><br>
<br>
</tt></font><font size="+1"><tt><font size="+1"><tt>To access the
list of vignettes use '</tt><tt>vignette(package=</tt><tt>"FLa4a")'
from within your R session, or download from the webpage (<a
class="moz-txt-link-freetext"
href="http://www.flr-project.org/FLa4a/articles/index.html"><a class="moz-txt-link-freetext" href="http://www.flr-project.org/FLa4a/articles/index.html">http://www.flr-project.org/FLa4a/articles/index.html</a></a>).</tt><tt><br>
</tt></font><br>
</tt><tt>Additionally a large number of small bugs and
improvements were included in this version, new plots for
residuals, etc</tt><tt>. I won't claim the package is bug-free
as I don't believe such thing exists. So please report any odd
results you may find.<br>
</tt><tt><br>
A quick trial can be done with:<br>
<br>
# lib and data<br>
library(FLa4a)<br>
data(ple4)<br>
data(ple4.indices)<br>
# fit<br>
fit <- sca(ple4, ple4.indices)</tt></font><span class="no"><br>
# diagnostics<br>
res</span> <span class="kw"><-</span> <span class="fu">residuals</span>(<span
class="no">fit</span>, <span class="no">ple4</span>, <span
class="no">ple4.indices</span>)<br>
<font size="+1"><tt>plot(res)<br>
qqmath(res)<br>
plot(fit, ple4)<br>
plot(fit, ple4.indices)<br>
AIC(fit)<br>
BIC(fit)<br>
# summary<br>
stk <- ple4 + fit<br>
</tt></font><font size="+1"><tt>plot(stk) <br>
</tt><tt><br>
</tt><tt>As usu</tt><tt>al all comments are welcome.</tt><tt><br>
</tt><tt><br>
</tt><tt>Best </tt><tt>regards</tt><tt><br>
</tt><tt><br>
</tt><tt>EJ</tt></font><font size="+1"><br>
</font><font size="+1"><tt><br>
</tt><tt>PS: sorry for any cross posting</tt></font><font
size="+1"><br>
</font>
<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
Joint Research Centre (JRC), Sustainable resources directorate, Water and Marine Resources unit
TP 051, Via Enrico Fermi 2749
I-21027 Ispra (VA), Italy
Office : +39 0332 785311
Fax: +39 0332 789658
</pre>
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