Calculate (quasi-)extinction risk for a simulate object

Calculate (quasi-)extinction risk for a simulate object

Usage

pr_extinct(sims, threshold = 0, subset = NULL, times = NULL)

Arguments

sims

an object returned from simulate

threshold

integer or numeric denoting the threshold population size below which a population is considered functionally extinct. Defaults to 0

subset

integer vector denoting the population classes to include in calculation of population abundance. Defaults to all classes

times

integer vector specifying generations to include in calculation of extinction risk. Defaults to all simulated generations

Details

Quasi-extinction risk is the probability of decline below some specified abundance threshold. This probability is extracted from a simulate object as the proportion of replicate trajectories that fall below this threshold at any time step within a set period. Abundances can be specified for all population classes or for a subset of classes.

Examples

# define a basic population
nstage <- 5
popmat <- matrix(0, nrow = nstage, ncol = nstage)
popmat[reproduction(popmat, dims = 4:5)] <- c(10, 20)
popmat[transition(popmat)] <- c(0.25, 0.3, 0.5, 0.65)

# define a dynamics object
dyn <- dynamics(popmat)

# simulate with the default updater
sims <- simulate(dyn, nsim = 1000)

# calculate quasi-extinction risk at a threshold population size
#   of 100 individuals
pr_extinct(sims, threshold = 100)
#> [1] 1

# repeat previous but focused on 4 and 5 year olds only
pr_extinct(sims, threshold = 100, subset = 4:5)
#> [1] 1

# repeat previous but ignore first 10 years
pr_extinct(sims, threshold = 100, times = 11:51)
#> [1] 1