makeIPMmatrix: Builds IPM matrices.

In IPMpack: Builds and analyses Integral Projection Models (IPMs).

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.

See Also

makeIPMPmatrix,makeIPMFmatrix,makeIPMCmatrix, diagnosticsPmatrix, makeDiscreteTrans

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)")

IPMpack documentation built on May 2, 2019, 2:36 a.m.