Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 | meanLifeExpect(IPMmatrix)
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IPMmatrix |
an IPMmatrix object defining survival transitions. |
Note that more complex approaches for discretely varying environments (e.g., as in Tuljapurkar & Horvitz 2006.) have yet to be implemented.
A vector of life expectancies each corresponding to a value of the size bins defined by Pmatrix@meshpoints.
C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans & Cory Merow.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | # 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=""))
}
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Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
[1] 1.259288 1.291546 1.322998 1.353213 1.381939 1.409107 1.434799 1.459219
[9] 1.482645 1.505385 1.527751 1.550029 1.572467 1.595273 1.618613 1.642618
[17] 1.667389 1.693009 1.719541 1.747038 1.775547 1.805105 1.835747 1.867505
[25] 1.900405 1.934472 1.969727 2.006190 2.043875 2.082796 2.122961 2.164377
[33] 2.207045 2.250965 2.296130 2.342528 2.390141 2.438938 2.488875 2.539882
[41] 2.591849 2.644602 2.697869 2.751231 2.804055 2.855421 2.904031 2.948137
[49] 2.985487 3.013327
[1] "Dim of envMatrix not equal to nEnvClass. Adjusted to 3"
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