mizer (version 3.4.0)

getParams: Extract the model state from a simulation

Description

A MizerParams object describes the state of the ecosystem: its species parameters, size grid, rate functions, and the current abundances stored in the initial_n, initial_n_pp, initial_n_other, and initial_effort slots. These functions extract that state from a MizerSim object.

Usage

getParams(sim, time_range, geometric_mean = FALSE)
initialParams(sim)
finalParams(sim)

Value

A MizerParams object with initial_n, initial_n_pp, initial_n_other, and initial_effort set to the values from the selected time of the simulation.

Arguments

sim

A MizerSim object.

time_range

The time range to average the abundances over. Can be a vector of values, a vector of min and max time, or a single value. Only the range of times is relevant, i.e., all times between the smallest and largest will be selected. Default is the final time step.

geometric_mean

If TRUE, the average of the abundances over the time range is a geometric mean instead of the default arithmetic mean. This does not affect the average of the effort or of other components, which is always arithmetic.

Details

getParams() returns the state averaged over a chosen time_range, or at a single time point. When no time_range is given, the state at the final time step is returned.

initialParams() returns the state at the initial time of the simulation, i.e., the MizerParams object that the simulation started from.

finalParams() returns the state at the last saved time step. It is a convenience wrapper around getParams() with no time_range argument.

The abundances set by getParams() are averages over the selected time range. By default this is an arithmetic mean; set geometric_mean = TRUE to use a geometric mean instead (this does not affect the effort or other components, which are always averaged arithmetically).

Examples

sim <- project(NS_params, t_max = 20, effort = 0.5)
# State at a specific time
params_10 <- getParams(sim, time_range = 10)
# State averaged over the last 10 years
params_avg <- getParams(sim, time_range = c(10, 20))
# State at the start and at the end of the simulation
params_start <- initialParams(sim)
params_end <- finalParams(sim)