Calculate (quasi-)extinction risk for a simulate
object
pr_extinct(sims, threshold = 0, subset = NULL, times = NULL)an object returned from simulate
integer or numeric denoting the
threshold population size below which a population is considered
functionally extinct. Defaults to 0
integer vector denoting the population classes
to include in calculation of population abundance. Defaults to
all classes
integer vector specifying generations to
include in calculation of extinction risk. Defaults to all
simulated generations
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.
# 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