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Last data update: 2014.03.03

R: Builds IPM matrices.

makeIPMmatrix

R Documentation

Builds IPM matrices.

Description

Uses survival/growth, fecundity and optionally clonal kernels to make an IPM kernel.

Usage

makeIPMmatrix(Pmatrix,Fmatrix,Cmatrix=NULL)

Arguments

`Pmatrix`	A survival/growth kernel constructed with makeIPMPmatrix().
`Fmatrix`	A fecundity kernel constructed with makeIPMFmatrix().
`Cmatrix`	A clonal kernel, constructed with makeIPMCmatrix(). Defaults to NULL since clonal reproduction may not be applicable for many species.

Details

A convenience function that makes an IPM kernel from the component kernels with all the same slots. All kernels being combined must have the same dimension, i.e. dim(Pmatrix@.Data) is the same as dim(Fmatrix@.Data).

Value

an object of class IPMmatrix with dimensions nBigMatrix*nBigMatrix, or nbig.matrix+nrow(discreteTrans).

Author(s)

Cory Merow, C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans & Cory Merow.

References

Easterling, Ellner & Dixon. 2000. Size-specific sensitivity: a new structured population model. Ecology 81, p694-708.

Ellner & Rees. 2006. Integral projection models for species with complex demography. The American Naturalist 167, p410-428.

For information on P matrix: Caswell. 2001. Matrix population models: construction, analysis, and interpretation. 2nd ed. Sinauer. p110-112.

For information on unintentional eviction from IPMs (which the various corrections try and account for) see Williams et al. 2012 Avoiding unintentional eviction from integral projection models. Ecology.

Examples

dff <- generateData()
Pmatrix <- makeIPMPmatrix(
						growObj = makeGrowthObj(dff), 
						survObj = makeSurvObj(dff),
						nBigMatrix=20,
						minSize = min(dff$size, na.rm = TRUE), 
						maxSize=max(dff$size, na.rm=TRUE))	
dff$fec[dff$fec==0] <- NA
fv1 <- makeFecObj(dff, Formula = fec~size, Transform = "log")
Fmatrix <- makeIPMFmatrix(
						fecObj = fv1, 
						nBigMatrix = 20, 
						minSize = min(dff$size, na.rm = TRUE), 
						maxSize = max(dff$size, na.rm = TRUE))
IPMmatrix <- makeIPMmatrix(Pmatrix,Fmatrix)
slotNames(IPMmatrix)

require(fields)
par(mfrow=c(2,2))
image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(Pmatrix), 
	xlab = "Size(t)", 
	ylab = "Size(t+1)",
	main = "Survival/Growth Kernel")
image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(Fmatrix), 
	xlab = "Size (t)", 
	ylab = "Size(t+1)",
	main = "Fecundity Kernel")
image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(IPMmatrix), 
	xlab = "Size(t)", 
	ylab = "Size(t+1)",
	main = "IPM Kernel")
# trick to visualize the whole IPM kernel when the Fmatrix has values>>Pmatrix
image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(IPMmatrix)^.1, 
	xlab = "Size(t)", 
	ylab = "Size(t+1)",
	main = "IPM Kernel^(.01)")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(IPMpack)
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IPMpack/makeIPMmatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeIPMmatrix
> ### Title: Builds IPM matrices.
> ### Aliases: makeIPMmatrix
> 
> ### ** Examples
> 
> dff <- generateData()
> Pmatrix <- makeIPMPmatrix(
+ 						growObj = makeGrowthObj(dff), 
+ 						survObj = makeSurvObj(dff),
+ 						nBigMatrix=20,
+ 						minSize = min(dff$size, na.rm = TRUE), 
+ 						maxSize=max(dff$size, na.rm=TRUE))	
> dff$fec[dff$fec==0] <- NA
> fv1 <- makeFecObj(dff, Formula = fec~size, Transform = "log")
> Fmatrix <- makeIPMFmatrix(
+ 						fecObj = fv1, 
+ 						nBigMatrix = 20, 
+ 						minSize = min(dff$size, na.rm = TRUE), 
+ 						maxSize = max(dff$size, na.rm = TRUE))
> IPMmatrix <- makeIPMmatrix(Pmatrix,Fmatrix)
> slotNames(IPMmatrix)
[1] ".Data"          "nDiscrete"      "nEnvClass"      "nBigMatrix"    
[5] "meshpoints"     "env.index"      "names.discrete"
> 
> require(fields)
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
 # 'lakes' database. Type '?world' or 'news(package="maps")'.  #


> par(mfrow=c(2,2))
> image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(Pmatrix), 
+ 	xlab = "Size(t)", 
+ 	ylab = "Size(t+1)",
+ 	main = "Survival/Growth Kernel")
> image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(Fmatrix), 
+ 	xlab = "Size (t)", 
+ 	ylab = "Size(t+1)",
+ 	main = "Fecundity Kernel")
> image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(IPMmatrix), 
+ 	xlab = "Size(t)", 
+ 	ylab = "Size(t+1)",
+ 	main = "IPM Kernel")
> # trick to visualize the whole IPM kernel when the Fmatrix has values>>Pmatrix
> image.plot(IPMmatrix@meshpoints, IPMmatrix@meshpoints, t(IPMmatrix)^.1, 
+ 	xlab = "Size(t)", 
+ 	ylab = "Size(t+1)",
+ 	main = "IPM Kernel^(.01)")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>