setInitialValues: Set initial values to values from a simulation

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Set initial values to values from a simulation

Description

This is used to use the results from one simulation as the starting values for another simulation.

Usage

setInitialValues(params, sim, time_range, geometric_mean = FALSE)

Arguments

params	A MizerParams object in which to set the initial values
sim	A MizerSim object from which to take the values.
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 then 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

The initial abundances (for both species and resource) in the params object are set to the abundances in a MizerSim object, averaged over a range of times. Similarly, the initial effort in the params object is set to the effort in the MizerSim object, again averaged over that range of times. When no time range is specified, the initial values are taken from the final time step of the simulation.

If the model described by sim and params has additional components created with setComponent() then the values of these components are also averaged and copied to params.

The MizerSim object must come from a model with the same set of species and gears and other components and the same size bins as the MizerParams object. Otherwise an error is raised.

Value

The params object with updated initial values and initial effort. Because of the way the R language works, setInitialValues() does not make the changes to the params object that you pass to it but instead returns a new params object. So to affect the change you call the function in the form params <- setInitialValues(params, sim).

See Also

Other functions for setting parameters: gear_params(), setExtEncounter(), setExtMort(), setFishing(), setInteraction(), setMaxIntakeRate(), setMetabolicRate(), setParams(), setPredKernel(), setReproduction(), setSearchVolume(), species_params()

Examples

params <- NS_params
sim <- project(params, t_max = 20, effort = 0.5)
params <- setInitialValues(params, sim)

mizer documentation built on Oct. 17, 2024, 9:07 a.m.