aae.pop (version 0.2.0)

stochasticity: Specify environmental and demographic stochasticity in models of population dynamics

Description

Specify environmental stochasticity (random variation in vital rates) and demographic stochasticity (random variation in population outcomes).

Usage

environmental_stochasticity(masks, funs)
demographic_stochasticity(masks, funs)

Value

environmental_stochasticity or

demographic_stochasticity object specifying the way in which stochasticity should be included in a matrix population model; for use with dynamics

Arguments

masks

a logical matrix or vector (or list of these) defining cells affected by funs. See Details and masks

funs

a function or list of functions with one element for each element of masks. See Details

Details

Masks must be of the same dimension as the population dynamics matrix (in the case of environmental stochasticity) or have one element for each class (in the case of demographic stochasticity). Masks specify cells influenced by stochasticity according to funs. Additional details on masks are provided in masks.

Functions must have at least one argument, a population dynamics matrix for environmental stochasticity or a vector of population abundances for demographic stochasticity. Functions must return an output of the same dimensions as the input, modified to reflect the effects of stochasticity on vital rates or population abundances.

Additional arguments to functions are supported and can be passed to simulate with the args, args.dyn, or args.fn arguments.

Examples

# define a population matrix (columns move to rows)
nclass <- 5
popmat <- matrix(0, nrow = nclass, ncol = nclass)
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)

# note that there is only one trajectory now because
#   this simulation is deterministic.
#
# let's change that by adding some environmental stochasticity
envstoch <- environmental_stochasticity(
  masks = list(
    reproduction(popmat, dims = 4:5),
    transition(popmat)
  ),
  funs = list(
    \(x) rpois(n = length(x), lambda = x),
    \(x) runif(n = length(x), min = 0.9 * x, max = pmin(1.1 * x, 1))
  )
)

# update the dynamics object and simulate from it
dyn <- update(dyn, envstoch)
sims <- simulate(
  dyn,
  init = c(50, 20, 10, 10, 5),
  nsim = 100,
  options = list(ntime = 50),
)

# a simple way to add demographic stochasticity is to change
#   the "updater" that converts the population at time t
#   to its value at time t + 1. The default in aae.pop
#   uses matrix multiplication of the vital rates matrix
#   and current population. A simple tweak is to update
#   with binomial draws. Note that this also requires a
#   change to the "tidy_abundances" option so that population
#   abundances are always integer values.
sims <- simulate(
  dyn,
  init = c(50, 20, 10, 10, 5),
  nsim = 100,
  options = list(
    update = update_binomial_leslie,
    tidy_abundances = floor
  )
)