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Dear Elena,<br>
<br>
thank you for your question and for showing a subset of your data. <br>
<br>
ad 2: It might be that you have rethink how you are breaking down
sexual reproduction in your system into separate steps. How are your
'number of flowers' and 'number of fruits' variables related? Does
every fruit result in a new, established plant by the end of the
time step? If so, then I can imagine that your population is
exploding in size.<br>
<br>
On the other hand, if the number of fruits per flower is a constant,
it should be added with the 'fecConstants' argument in 'makeFecObj'.
Also the per-seed-seedling-establishment-rate can be added in
'fecConstants'. Good that you studied the second chapter of the
appendix to Merow et al. 2014, which contains an example with
IPMpack-code that seems relevant for your species as well:
<a class="moz-txt-link-freetext" href="http://tinyurl.com/ndkh99r">http://tinyurl.com/ndkh99r</a><br>
<br>
Perhaps it is a good idea to discuss your species' life cycle with
your advisors.<br>
<br>
best wishes,<br>
Eelke<br>
<br>
PS: ad 1: It might be that you have rather few deaths in your
dataset, making it hard for binomial regression models to fit all
parameters. However, it might also be that you are having
difficulties with reading your data into R, unrelated to IPMpack.<br>
<br>
<br>
<div class="moz-cite-prefix">On 09/02/15 18:04, Elena S. wrote:<br>
</div>
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<div dir="ltr">Hi everybody,<br>
<br>
<span id="result_box" lang="en"><span>Congratulation for the
pack, is very useful. <br>
</span></span>I'm a PhD student that use I<span
id="result_box" lang="en"><span class="hps">PMpack</span> <span
class="hps">to analyze</span> <span class="hps">different
populations</span> <span class="hps">of</span> a <span
class="hps">perennial plant species</span><span> (so I have
3 years of data for every population). <br>
</span> <br>
<span class="hps">I have two questions</span><span>:</span><br>
<span class="hps">1)</span> <span class="hps">in one of the</span>
<span class="hps">populations</span> I <span class="hps">have</span>
many <span class="hps">NA</span><span>,</span> <span
class="hps">both in</span> <span class="hps">size</span> <span
class="hps">and in</span> <span class="hps">sizeNext</span><span>
columns, consequently</span> <span class="hps">also</span>
<span class="hps">in</span> <span class="hps">fec0</span> <span
class="hps atn">(</span><span>probability of</span> <span
class="hps">flowering)</span> <span class="hps">and</span>
<span class="hps">fec1</span> <span class="hps atn">(</span><span>number
of fruit</span><span>)</span><span>.</span> <br>
<span class="hps">In the construction</span> <span
class="hps">of</span> <span class="hps">models</span> <span
class="hps">of</span> <span class="hps">survival</span> <span
class="hps">and</span> <span class="hps">growth</span> <span
class="hps atn">(</span><span>via</span> <span class="hps">survModelComp</span>
<span class="hps">and</span> <span class="hps">growthModelComp</span><span>)</span>
<span class="hps">I get the following</span> <span
class="hps">error</span><span>: <br>
"Error</span> <span class="hps">in</span> <span
class="hps">plot.window</span> <span class="hps atn">(</span><span>...</span><span>)</span><span>:
need</span> <span class="hps">finite</span> <span
class="hps atn">'</span><span>ylim</span><span>'</span> <span
class="hps">values</span><br>
<span class="hps">In</span> <span class="hps">addition:</span>
<span class="hps">There</span> <span class="hps">were</span>
<span class="hps">16</span> <span class="hps">warnings</span>
<span class="hps atn">(</span><span>use warnings</span> <span
class="hps atn">(</span><span>)</span> <span class="hps">to</span>
<span class="hps">see</span> <span class="hps">them</span><span>)</span><span>."</span>
<span class="hps"><br>
Here </span><span class="hps">the code</span> <span
class="hps">(which works</span> <span class="hps">well with</span>
<span class="hps">other</span> populations<span>,</span> <span
class="hps">except</span> <span class="hps">with</span> <span
class="hps">this</span><span>)</span><span>:</span><br>
<span class="hps">survModelComp</span> <span class="hps atn">(</span><span>dataf</span>
<span class="hps">=</span> <span class="hps">dhsr</span><span>,</span>
<span class="hps"></span><span class="hps">makePlot</span> <span
class="hps">=</span> <span class="hps">TRUE</span><span>, </span><span
class="hps">legendPos</span> <span class="hps">=</span> <span
class="hps atn">"</span><span>bottomleft</span><span>", </span><span
class="hps">Maintitle</span> <span class="hps">=</span> <span
class="hps atn">"</span><span>Survival</span><span>"</span><span>)<br>
It is possible that the many NAs create a problem?<br>
</span><br>
<span class="hps">2)</span> <span class="hps">in all </span></span><span
id="result_box" lang="en"><span class="hps"><span
id="result_box" lang="en"><span class="hps">analyzed</span>
<span class="hps"></span></span> populations</span> <span
class="hps">lambda</span> <span class="hps">get</span> <span
class="hps">very high</span> <span class="hps">as many</span>
<span class="hps">variables</span> <span class="hps">added</span>
<span class="hps">in</span> <span class="hps">fecundity</span>
<span class="hps">object</span><span>.</span> <br>
<span class="hps">I tried</span> <span class="hps">inserting</span>
<span class="hps">the</span> <span class="hps">data frame</span>
<span class="hps">columns</span><span>:</span><br>
<span class="hps">fec0</span> <span class="hps">(probability
of</span> <span class="hps">flowering)</span><span>,</span>
<span class="hps">fec1</span> <span class="hps">(number of</span>
<span class="hps">fruits</span><span>)</span><span>,</span> <span
class="hps">nFl</span> <span class="hps">(number of</span>
<span class="hps">flowers</span><span>)</span><span>.</span><br>
<span class="hps">I get a</span> <span class="hps">lambda</span><span>
near </span><span class="hps">1</span> <span class="hps">only
if</span> <span class="hps">I leave</span> <span
class="hps">exclusively</span> <span class="hps">fec0</span>
<span class="hps atn">(</span><span>the probability of</span>
<span class="hps">flowering)</span><span>,</span> <span
class="hps">does anyone know how</span> <span class="hps">to</span>
<span class="hps">solve</span> <span class="hps">by adding</span>
<span class="hps">at least</span> <span class="hps">fec1</span><span>?</span></span><br>
R0 also get <span id="result_box" class="short_text" lang="en"><span
class="hps">excessively high values... I think that is for
the same problem with lambda.</span></span><br>
<br>
Thanks to all for any suggestion,<br>
<br>
Best wishes,<br>
<br>
Elena Sulis </div>
<br>
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