aae.pop (version 0.2.0)

dynamics: Create and update population dynamics objects

Description

Define population dynamics from a matrix and additional objects that determine covariate effects, density dependence, and forms of stochasticity.

Usage

dynamics(matrix, ...)
# S3 method for dynamics
update(object, ...)
is.dynamics(x)

Value

dynamics object containing a matrix population model and all associated processes

Arguments

matrix

a matrix of vital rates specifying transitions between ages or stages. Specified in the format ntp1 = A A is the matrix and nt is the vector of abundances, so that values in a given column and row denote a transition from that column to that row

...

additional objects used to define population dynamics. Must be one or more of covariates, replicated_covariates, environmental_stochasticity, demographic_stochasticity, density_dependence, add_remove_pre, or add_remove_post. Note that density_dependence_n is equivalent to add_remove_post.

object

a dynamics object

x

an object to pass to is.dynamics

Details

A call to dynamics defines an object of class dynamics, which can be used to simulate population trajectories with the simulate function. The plot function is supported and will generate a general life-cycle diagram based on the defined population dynamics.

A compiled dynamics object can be updated to change any of the included processes with the update function.

Examples

# define a population
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)

# and plot this
if (rlang::is_installed("DiagrammeR")) {
  plot(dyn)
}