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<div class="">Dear Karina,</div>
<div class="">You’d log-transform the data for visual purposes only, and at the very end of the IPM construction/discretization. See example below.</div>
<div class="">cheers</div>
<div class="">
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rob s-g</div>
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<div>library(IPMpack)</div>
<div><br class="">
</div>
<div>d <- generateData()</div>
<div><br class="">
</div>
<div>Pmatrix <- makeIPMPmatrix(</div>
<div> growObj = makeGrowthObj(d), </div>
<div> survObj = makeSurvObj(d),</div>
<div> nBigMatrix=20,</div>
<div> minSize = min(d$size, na.rm = TRUE), </div>
<div> maxSize=max(d$size, na.rm=TRUE))</div>
<div><br class="">
</div>
<div>d$fec[d$fec==0] <- NA</div>
<div>fv1 <- makeFecObj(d, Formula = fec~size, Transform = "log")</div>
<div>Fmatrix <- makeIPMFmatrix(</div>
<div> fecObj = fv1, </div>
<div> nBigMatrix = 20, </div>
<div> minSize = min(d$size, na.rm = TRUE), </div>
<div> maxSize = max(d$size, na.rm = TRUE))</div>
<div><br class="">
</div>
<div>IPMmatrix <- makeIPMmatrix(Pmatrix,Fmatrix)</div>
<div><br class="">
</div>
<div>library(fields)</div>
<div><br class="">
</div>
<div>#Without log-transformation</div>
<div>image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(IPMmatrix), </div>
<div> xlab = "Size(t)", </div>
<div> ylab = "Size(t+1)",</div>
<div> main = "Survival/Growth Kernel")</div>
<div><br class="">
</div>
<div>#With log-transformation</div>
<div>image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(log(IPMmatrix)), </div>
<div> xlab = "Size(t)", </div>
<div> ylab = "Size(t+1)",</div>
<div> main = "Survival/Growth Kernel")</div>
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<br class="">
<br class="">
New book on the Evolution of Senescence in the Tree of Life <a href="http://tinyurl.com/SenescenceBook" class="">http://tinyurl.com/SenescenceBook</a><br class="">
<br class="">
"Aliud iter ad prosperitatem nos est: id est omnibus rebus vincere"<br class="">
.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.<br class="">
Dr Rob Salguero-Gómez<br class="">
<br class="">
Oxford - NERC Independent Research Fellow<br class="">
University of Queensland - Honorary Research Fellow<br class="">
Max Planck Institute for Demographic Research - Guest Researcher<br class="">
<br class="">
<a href="http://sites.google.com/site/RobResearchSite/" class="">http://sites.google.com/site/RobResearchSite/</a></div>
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<div class="">Today's Topics:<br class="">
<br class="">
1. How do you represent a P kernel on a log scale? (Karina Scavo)<br class="">
<br class="">
<br class="">
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<br class="">
Message: 1<br class="">
Date: Tue, 23 May 2017 14:45:43 -0400<br class="">
From: Karina Scavo <<a href="mailto:kscavo@bu.edu" class="">kscavo@bu.edu</a>><br class="">
To: <a href="mailto:ipmpack-users@r-forge.wu-wien.ac.at" class="">ipmpack-users@r-forge.wu-wien.ac.at</a><br class="">
Subject: [Ipmpack-users] How do you represent a P kernel on a log<br class="">
<span class="Apple-tab-span" style="white-space: pre;"></span>scale?<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space: pre;"></span><<a href="mailto:CAM0_wNh+wXmHTuUBKpLwyGRyHo7SM7z-r=-6r+QAio7SYX7Jhg@mail.gmail.com" class="">CAM0_wNh+wXmHTuUBKpLwyGRyHo7SM7z-r=-6r+QAio7SYX7Jhg@mail.gmail.com</a>><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Hi all,<br class="">
<br class="">
I have created a P matrix that when plotted, looks similar to Figure 3.8 in<br class="">
the appendix of the paper, "Advancing population ecology with integral<br class="">
projection models: a practical guide" by Merow et al 2014 (see attached).<br class="">
The information in the appendix says it would be best to represent this<br class="">
kernel on a log scale.<br class="">
<br class="">
How do you transform this kernel on a log scale? Do you do it at the stage<br class="">
of making the P matrix (in makeIPMPmatrix) or at when making the growth and<br class="">
survival objects?<br class="">
<br class="">
Any help would be appreciated!<br class="">
<br class="">
Best,<br class="">
<br class="">
Karina<br class="">
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