sampleIPMOutput: Gets IPM output from a list of P matrices (only survival and...

In wpetry/IPMpack2: Builds and analyses Integral Projection Models (IPMs).

Gets IPM output from a list of P matrices (only survival and size information) or full IPMs (P matrices + F matrices; the latter include sexual reproduction information).

Description

Gets synthetic values including life expectancy, passage time, and, if a fecundity matrix is available, population growth rate (lambda), stable stage distribution, reproductive output, etc. It is helpful when building multiple IPMs for study of parameter uncertainty or stochastic dynamics.

Usage

sampleIPMOutput(IPMList=NULL,PMatrixList=NULL,passageTimeTargetSize=c(), 
sizeToAgeStartSize=c(),sizeToAgeTargetSize=c(),warn=TRUE)

Arguments

IPMList	List of survival-size IPM matrices for which summary statistics desired. When this information is included, population growth rate (lambda), and stable stage distribution will be provided.
PMatrixList	List of survival-growth (P) matrices for which summary statistics desired. When this information is included, only passage time and sizeToAge calculations will be provided
passageTimeTargetSize	Target size for passage time. If none is provided defaults to the median of the IPM meshpoints.
sizeToAgeStartSize	Starting size to determine the expected age which sizeToAgeTargetSize will be reached. If none is provided defaults to the minimum of the IPM meshpoints.
sizeToAgeTargetSize	Target size to determine the expected age which sizeToAgeTargetSize will be reached. If none is provided defaults to the IPM meshpoints.
warn	turn warning messages on/off.

Value

LE	matrix of life expectancies, columns correspond to meshpoints, rows corresponding to each element of the list of P matrices
pTime	matrix of passage times to the targetSize from each of the meshpoints (columns) and for each element in the P matrix list (columns).
lambda	vector of population growth rates corresponding to value obtained combining each element of the list of P matrices with the corresponding element in the list of F matrices; if no F matrix list is provided, it returns a vector of NAs.
stableStage	matrix of stable stage distributions rows corresponding to values obtained. combining each element of the list of Pmatrices with the corresponding element in the list of Fmatrices; if no Fmatrix list is provided, this is a matrix of NAs.
meshpoints	matrix meshpoints.
resSize	matrix providing target sizes for size to age estimate (assuming age=1 at sizeStart), of length nsizeToAge space equally between the smallest and largest meshpoints.
resAge	matrix providing time in time-steps to get to resSize, rows corresponding sequential elements in the list of P matrices.

Note

This function has replaced the functionality of getIPMoutput and getIPMoutputDirect. Those functions are no longer supported but have been hidden (.getIPMoutput and .getIPMoutputDirect) and can be accessed for backward compatibility.

Author(s)

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

References

Zuidema, Jongejans, Chien, During & Schieving. Integral projection models for trees: a new parameterization method and a validation of model output. Journal of Ecology 98, p345-355.

See Also

sampleIPM, sampleVitalRateObj, sampleSequentialIPMs

Examples

# ===========================================================================
# Sample Vital Rate Objects
	# Parametric bootstrap sample for a growth object 
		dff <- generateData(type='discrete')
		gr1 <- makeGrowthObj(dff)
		gr1List=sampleVitalRateObj(gr1,nSamp=9)

	# Parametric bootstrap sample for a survival object 
		sv1 <- makeSurvObj(dff)
		sv1List=sampleVitalRateObj(sv1,nSamp=9)

	# Parametric bootstrap sample for a fecundity object 
		fv1 <- makeFecObj(dff)
		fv1List=sampleVitalRateObj(
			fv1,nSamp=9,
			nDiscreteOffspringTransitions =100,
			nOffspring=100)

	# Parametric bootstrap sample for a discrete transition object 
		dt1 <- makeDiscreteTrans(dff)
		dt1List=sampleVitalRateObj(
			dt1,nSamp=9,
			nDiscreteGrowthTransitions=100)
# ===========================================================================
	# Make a list of growth/survival (P) matrices (omitting fecundity)
		Pmatrixlist=sampleIPM(
			growObjList=gr1List,
			survObjList=sv1List,
			fecObjList =NULL,
			nBigMatrix = 20, minSize = -5, maxSize = 20)
		# plot results
		par(mfrow=c(3,3))
		lapply(Pmatrixlist,image)

	# Combine the list of fecundity objects with a single survival 
	# and growth object in a list of IPMs to look at just the impact 
	# of uncertainty in fecundity parameter estimates on population growth rate
		IPMlist2=sampleIPM(
			growObjList=list(gr1),
			survObjList=list(sv1),
			fecObjList =fv1List,
			discreteTransList=list(dt1), 
			nBigMatrix = 20, minSize = -5, maxSize = 20)
		# plot results
		lapply(IPMlist2,image) 

	# Combine the lists of all vital rate objects in a list of IPMs 
	# to look at the impact of uncertainty in all parameters on population 
	# growth rate
		IPMlist3=sampleIPM(
			growObjList=gr1List,
			survObjList=sv1List,
			fecObjList =fv1List,
			discreteTransList=list(dt1),
			nBigMatrix = 20, minSize = -5, maxSize = 20)
		# plot results
		lapply(IPMlist3,image) 

# ===========================================================================
# Summarize the outputs	
	# Get uncertainty in passage time from the list of growth/survival matrices
		IPMout1=sampleIPMOutput(PMatrixList=Pmatrixlist)
		qLE=apply(IPMout1[['LE']],2,quantile,probs=c(.025,.5,.975))
		plot(IPMout1$meshpoints,qLE[2,],type='l',ylim=c(0,max(qLE)))
		lines(IPMout1$meshpoints,qLE[1,],type='l',lty=3)
		lines(IPMout1$meshpoints,qLE[3,],type='l',lty=3)

	# Get uncertainty in lambda from the list of IPMs where only 
	# fecundity varied
		IPMout2=sampleIPMOutput(IPMList=IPMlist2)
		qlambda=quantile(IPMout2[['lambda']],probs=c(.025,.5,.975))
		boxplot(IPMout2[['lambda']])
	
	# Get uncertainty in lambda and passage time from size 5 to a 
	# series of size from the list of IPMs where all vital rates varied
		IPMout3=sampleIPMOutput(
			IPMList=IPMlist3,
			passageTimeTargetSize=c(10),
			sizeToAgeStartSize=c(5),
			sizeToAgeTargetSize=c(6,7,8,9,10))
		qlambda=quantile(IPMout3[['lambda']],probs=c(.025,.5,.975))
		boxplot(IPMout3[['resAge']])  

wpetry/IPMpack2 documentation built on Sept. 29, 2022, 9:41 a.m.