Description Usage Arguments Value Note Author(s) References Examples
Method to calculate population growth rate (lambda) and stable stage distribution where a large number of bins are used in the IPM, as it may be the case with species that vary largely in size, or models that include size x age interactions.
1 | largeMatrixCalc(Pmatrix, Fmatrix, tol = 1e-08)
|
Pmatrix |
object of class IPMmatrix describing survival transitions. |
Fmatrix |
object of class IPMmatrix describing fecundity transitions. |
tol |
tolerance for convergence, defaults to 1e-08. |
lambda |
Population rate of increase. |
stableDist |
Stable stage distribution. |
h1 |
size bin width. |
Modified from Appendix A in Rees and Ellner 2009 (see references).
C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans & Cory Merow.
Rees and Ellner. 2009. Integral projection models for populations in temporally varying environments. The American Naturalist 79, p575-594.
Caswell. 2001. Matrix population models: construction, analysis, and interpretation. 2nd ed. Sinauer. p377-502.
Garcia, Dahlgren, Ehrlen. 2011. No evidence of senescence in a 300-year-old mountain herb. Journal of Ecology 99, p1424-1430.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | dff <- generateData()
Pmatrix <- makeIPMPmatrix(minSize = min(dff$size, na.rm = TRUE),
maxSize = max(dff$size, na.rm = TRUE), growObj = makeGrowthObj(dff),
survObj = makeSurvObj(dff))
Fmatrix <- makeIPMFmatrix(minSize = min(dff$size, na.rm = TRUE),
maxSize = max(dff$size, na.rm = TRUE),fecObj = makeFecObj(dff))
largeMatrixCalc(Pmatrix, Fmatrix)
par(mfrow=c(1,2),pty="s")
plot(largeMatrixCalc(Pmatrix, Fmatrix)$stableDist,
ylab = "Stable stage distribution",
xlab = "Continuous (e.g. size) stage",
type = "l", col = "blue", lty = 1, ylim = c(0:1))
#Note that this will not always run - as tolerance levels
# for convergence are set to be quite high
#plot(largeMatrixCalc(Pmatrix, Fmatrix)$reprodValue,
# ylab = "Reproductive value",
# xlab = "Continuous (e.g. size) stage", type = "l", col = "red",
# lty = 1, ylim = c(0:1))
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