Calculate expected minimum population size (EMPS) for a simulate object

Calculate expected minimum population size (EMPS) for a simulate object

Usage

emps(sims, subset = NULL, times = NULL, fun = mean, ...)

Arguments

sims

an object returned from simulate

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

fun

function used to calculate average over all replicate trajectories. Defaults to mean. Alternatives might include median or min

...

additional arguments passed to fun

Details

Expected minimum population size (EMPS) is the average minimum value of all replicate trajectories. This value represents an expected lower bound on population sizes over all generations, accounting for variation among replicates. 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 expected minimum population size
emps(sims)
#> [1] 35.67922

# calculate expected minimum population size for 4 and 5 year
#   olds only
emps(sims, subset = 4:5)
#> [1] 1.31996

# calculate expected minimum population size but ignore first 10 years
emps(sims, times = 11:51)
#> [1] 36.02284

# calculate expected minimum population size based on median
emps(sims, fun = median)
#> [1] 35.69241