meanLifeExpect: Calculates the mean life expectancy.
In wpetry/IPMpack2: Builds and analyses Integral Projection Models (IPMs).

meanLifeExpect

R Documentation

Calculates the mean life expectancy.

Description

Provided a P matrix, which defines survival transitions across stages, this function outputs a vector defining life expectancy in units of the time step used (see convertIncrement()), for each of the size bins.

Usage

meanLifeExpect(IPMmatrix)

Arguments

IPMmatrix

an IPMmatrix object defining survival transitions.

Details

Note that more complex approaches for discretely varying environments (e.g., as in Tuljapurkar & Horvitz 2006.) have yet to be implemented.

Value

A vector of life expectancies each corresponding to a value of the size bins defined by Pmatrix@meshpoints.

Author(s)

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

References

Caswell, 2001. Matrix population models: analysis, construction and interpretation. 2nd ed. Sinauer. p118-120.

Cochran & Ellner. 1992. Simple methods for calculating age-based life history parameters for stage-structured populations. Ecological Monographs 62, p345-364.

Tuljapurkar & Horvitz. 2006. From stage to age in variable environments. Life expectancy and survivorship. Ecology 87, p1497-1509.

Examples

# With a single continuous state variable (e.g. size):
dff <- generateData()
Pmatrix <- makeIPMPmatrix(minSize = min(dff$size, na.rm = TRUE),
maxSize = max(dff$size, na.rm = TRUE), growObj=makeGrowthObj(dff),
survObj = makeSurvObj(dff))
meanLifeExpect(Pmatrix)

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

plot(meanLifeExpect(Pmatrix), ylab = "Mean life expectancy", 
xlab = "Continuous (e.g. size) stage", type = "l", col="dark gray", 
ylim = c(0,max(meanLifeExpect(Pmatrix))))

# With continuous (e.g. size) and discrete (e.g. seedbank) stages:
dff <- generateData(type="discrete")
dff$covariate <- sample(1:3, size = nrow(dff), replace = TRUE)
dff$covariateNext <- sample(1:3, size = nrow(dff), replace = TRUE)
discM <- makeDiscreteTrans(dff)
Pmatrix <- makeCompoundPmatrix(minSize = min(dff$size, na.rm = TRUE), 
maxSize = max(dff$size, na.rm = TRUE), envMatrix = makeEnvObj(dff),
growObj = makeGrowthObj(dff, Formula = sizeNext~size+size2+covariate),
survObj = makeSurvObj(dff, Formula = surv~size+size2+covariate), 
discreteTrans = discM)
mLE <- meanLifeExpect(Pmatrix)

# showing three environments on different panels, 
# life expectancy of discrete stages
# shown at level of the first size class
par(mfrow=c(max(Pmatrix@env.index),1))

xvals <- c(rep(Pmatrix@meshpoints[1],ncol(discM@discreteTrans)-1),
    Pmatrix@meshpoints)

for (k in 1:max(Pmatrix@env.index)) { 
	indx <- ((k-1)*(ncol(discM@discreteTrans)-1+length(Pmatrix@meshpoints))+1):
		(k*(ncol(discM@discreteTrans)-1+length(Pmatrix@meshpoints)))
	
	plot(xvals,mLE[indx], 
		ylab = "Mean life expectancy", 
		xlab = "Continuous (e.g. size) and discrete (e.g. seedbank) stages", 
		type = "l", col = "dark gray", ylim = c(0,max(mLE)), 
		main=paste("habitat ",k,sep=""))	
	}

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