aae.pop (version 0.2.0)

updaters: Functions for a single time-step update

Description

Define how population abundances are updated from one time step to the next. Functions can take any form but will only be vectorised across replicates in limited situations.

Usage

update_crossprod(pop, mat)
update_binomial_leslie(pop, mat)
update_multinomial(pop, mat)

Value

a matrix containing population abundances in each stage of a matrix population model. Contains one row for each replicate population trajectory and one column for each population stage

Arguments

pop

current state of the population

mat

matrix of vital rates used to update population state

Details

Updaters can be changed through the options argument to simulate and can also be changed globally for an R session by changing the global option with, e.g., options(aae.pop_update = update_binomial_leslie)

update_crossprod updates abundances with a direct matrix multiplication that does not include any form of demographic stochasticity. This is the fastest update option and will vectorise across replicates if the population matrix is not expanded by environmental_stochasticity or density_dependence.

update_binomial_leslie updates abundances with a direct RNG draw that combines update with demographic stochasticity, assuming a Leslie matrix.

update_multinomial updates abundances with a direct RNG draw that combines update with demographic stochasticity, allowing for general matrix forms (slower than update_binomial_leslie).

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)

# simulate with a multinomial updater
sims <- simulate(dyn, options = list(update = update_multinomial))