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<p>Thank you Iago. 'simplify' is exactly what I was looking for.
Yes, I am using F values (not hr).</p>
<p> I was indeed plotting the stock object with lattice-based plot
before (which seemed to sum the Fs for a single yearly F value).
The ggplotFL version looks much nicer, although I'm getting some
strange plots when applying it to the non-simplified version (with
season dimension). I will also look further into this - as it may
have to do with some NAs (or an occasional Inf)...</p>
<p>I'll let you know how things go and try and organize my
questions.</p>
<p>Cheers, Marc<br>
</p>
<p><br>
</p>
<pre class="moz-signature" cols="72">Dr. Marc Taylor
Marine Lebende Resourcen / Marine Living Resources
Thünen-Institut für Seefischerei / Thünen Institute of Sea Fisheries
Herwigstraße 31
27572 Bremerhaven, Germany
Tel: +49 471 94460-252
Mail: <a class="moz-txt-link-abbreviated" href="mailto:marc.taylor@thuenen.de">marc.taylor@thuenen.de</a>
Web: <a class="moz-txt-link-abbreviated" href="http://www.thuenen.de">www.thuenen.de</a></pre>
<div class="moz-cite-prefix">On 31-Aug-18 10:13 AM, Iago Mosquera
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1535697242.local-e3073195-40e8-v1.4.2-f587b7b7@getmailspring.com">
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<div>Hi,</div>
<br>
<div>Q1<span data-emoji-typing="true">:</span> Yes. For an FLStock
there is a simplify() method, which you can call with</div>
<br>
<div>simplify(stock, dims="season")</div>
<br>
<div>and will take abundances in season 1 to represent the whole
year, add up catches, and calculate a weighted mean across wts.
It will then calculate harvest from survivors.</div>
<br>
<div>Have a go and let me know, it might need a bit more testing.</div>
<br>
<div>Q2<span data-emoji-typing="true">:</span> Are you using F or
HR? If F, then usually values are for the time period specified,
be it a month or a year<span data-emoji-typing="true">:</span>
the value that would get you survivors at the end of the period
from numbers at the start using N <em> exp(-1</em>(F + M)).</div>
<br>
<div>The FLStock plot in ggplotFL deals with seasonal objects, are
you using the lattice-based one in FLCore?</div>
<br>
<div>I am dealing at the moment with seasonal FLStock objects, and
even running seasonal forecasts wth FLasher. Happy to see if it
all works for you.</div>
<br>
<div>Cheers,</div>
<br>
<br>
<div>Iago</div>
<br>
<div class="gmail_quote_attribution">On Aug 31 2018, at 8:07 am,
Marc Taylor <a class="moz-txt-link-rfc2396E" href="mailto:marc.taylor@thuenen.de"><marc.taylor@thuenen.de></a> wrote:</div>
<blockquote><br>
<div>
<div>I am using an FLStock object to record information from a
simulation</div>
<div>model that is run at monthly time increments; i.e. the
@season dimension</div>
<div>equals 12.</div>
<br>
<div>Q1. Is there a function in FLCore that can compute the
yearly values</div>
<div>(i.e. collapse the season dimension)? I would write one
for my purposes</div>
<div>if this doesn't exist, but I wanted to ask first. As far
as I know,</div>
<div>there are only the compute functions for specific slots
(e.g.</div>
<div>computeCatch), but not ones that operate on the whole
object at once.</div>
<br>
<div>Q2. How would you recommend that I record mortality at
the season (i.e.</div>
<div>monthly) level: I started off at having their units be
"per year" rates,</div>
<div>but the default plot(stock) appears to sum the mortality
values for the</div>
<div>yearly time series, rather than to average them, which
would suggest</div>
<div>keeping them in "per season" units. This also seems to be
consistent</div>
<div>with the output of SMS (one sums the seasonal values to
arrive at the</div>
<div>yearly ones).</div>
<br>
<div>Hope these questions are clear for you!</div>
<br>
<div>Cheers, Marc</div>
<br>
<div>--</div>
<div>Dr. Marc Taylor</div>
<div>Marine Lebende Resourcen / Marine Living Resources</div>
<div>Thünen-Institut für Seefischerei / Thünen Institute of
Sea Fisheries</div>
<div>Herwigstraße 31</div>
<div>27572 Bremerhaven, Germany</div>
<br>
<div>Tel: +49 471 94460-252</div>
<div>Mail: <a class="moz-txt-link-abbreviated" href="mailto:marc.taylor@thuenen.de">marc.taylor@thuenen.de</a></div>
<div>Web: <a class="moz-txt-link-abbreviated" href="http://www.thuenen.de">www.thuenen.de</a></div>
<br>
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