stochGrowthRateSampleList: Estimating the stochastic population growth rate (lambda_s) or invasion rat.

Description

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.

Usage

stochGrowthRateSampleList(nRunIn,tMax,listIPMmatrix=NULL,
					listPmatrix=NULL, listFmatrix=NULL,seedList=NULL,
					densDep=FALSE)

Arguments

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

Value

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.

References

Caswell, 2001. Matrix population models: analysis, construction and interpretation. 2nd ed. Sinauer. p452-502.

Examples

Run this code

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)