Description Usage Arguments Value Author(s) References See Also Examples
Estimates the stochastic growth rate (lambda_s) by iteration; operates by sampling a list of IPMs. Note that the function stoch.growth.rate in the package popbio does this more efficiently and with more useful output; but may fail for large bin numbers. If densDept is TRUE, estimates the stochastic invasion rate in the presence of density dependence in seedling establishment by iteration; operates by sampling a list of IPMs and recalculating the probability of seed establishment at each time-step.
1 2 3 |
nRunIn |
numeric, the size of the burnin, |
tMax |
numeric, the total samples desired. |
listIPMmatrix |
a list of IPMmatrix objects corresponding to possible states of the environment. |
listPmatrix |
a list of IPM P matrices corresponding to possible states of the environment. |
listFmatrix |
a list of IPM F matrices corresponding to possible states of the environment. |
seedList |
numeric, a vector of the number of successful recruit corresponding to possible states of the environment. |
densDep |
Boolean indicating whether density dependence in seedling establishment should be implemented |
a numeric converging on high enough log lambda_s for sufficient tMax; note that if the population size declines to zero, this may return NAs because of logging.
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. p452-502.
1 2 3 4 | dff <- generateData()
IPMlist <- sampleSequentialIPMs(dataf = dff, nBigMatrix = 10, minSize = -5,
maxSize = 15,fecConstants=data.frame(1e6), correction="constant")
stochGrowthRateSampleList(listIPMmatrix = IPMlist,nRunIn = 100, tMax = 5000)
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