[Ipmpack-users] How do you represent a P kernel on a log scale?

[Roberto Salguero-Gomez]

Dear Karina,
You’d log-transform the data for visual purposes only, and at the very end of the IPM construction/discretization. See example below.
cheers
rob s-g



library(IPMpack)

d <- generateData()

Pmatrix <- makeIPMPmatrix(
  growObj = makeGrowthObj(d),
  survObj = makeSurvObj(d),
  nBigMatrix=20,
  minSize = min(d$size, na.rm = TRUE),
  maxSize=max(d$size, na.rm=TRUE))

d$fec[d$fec==0] <- NA
fv1 <- makeFecObj(d, Formula = fec~size, Transform = "log")
Fmatrix <- makeIPMFmatrix(
  fecObj = fv1,
  nBigMatrix = 20,
  minSize = min(d$size, na.rm = TRUE),
  maxSize = max(d$size, na.rm = TRUE))

IPMmatrix <- makeIPMmatrix(Pmatrix,Fmatrix)

library(fields)

#Without log-transformation
image.plot(IPMmatrix at meshpoints, IPMmatrix at meshpoints, t(IPMmatrix),
           xlab = "Size(t)",
           ylab = "Size(t+1)",
           main = "Survival/Growth Kernel")

#With log-transformation
image.plot(IPMmatrix at meshpoints, IPMmatrix at meshpoints, t(log(IPMmatrix)),
           xlab = "Size(t)",
           ylab = "Size(t+1)",
           main = "Survival/Growth Kernel")



New book on the Evolution of Senescence in the Tree of Life http://tinyurl.com/SenescenceBook

"Aliud iter ad prosperitatem nos est: id est omnibus rebus vincere"
.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.
Dr Rob Salguero-Gómez

Oxford - NERC Independent Research Fellow
University of Queensland - Honorary Research Fellow
Max Planck Institute for Demographic Research - Guest Researcher

http://sites.google.com/site/RobResearchSite/





Today's Topics:

  1. How do you represent a P kernel on a log scale? (Karina Scavo)


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Message: 1
Date: Tue, 23 May 2017 14:45:43 -0400
From: Karina Scavo <kscavo at bu.edu<mailto:kscavo at bu.edu>>
To: ipmpack-users at r-forge.wu-wien.ac.at<mailto:ipmpack-users at r-forge.wu-wien.ac.at>
Subject: [Ipmpack-users] How do you represent a P kernel on a log
scale?
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Hi all,

I have created a P matrix that when plotted, looks similar to Figure 3.8 in
the appendix of the paper, "Advancing population ecology with integral
projection models: a practical guide" by Merow et al 2014 (see attached).
The information in the appendix says it would be best to represent this
kernel on a log scale.

How do you transform this kernel on a log scale? Do you do it at the stage
of making the P matrix (in makeIPMPmatrix) or at when making the growth and
survival objects?

Any help would be appreciated!

Best,

Karina
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