project: Project size spectrum forward in time

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Project size spectrum forward in time

Description

Runs the size spectrum model simulation. The function returns an object of type MizerSim that can then be explored with a range of summary_functions, indicator_functions and plotting_functions.

Usage

project(
  object,
  effort,
  t_max = 100,
  dt = 0.1,
  t_save = 1,
  t_start = 0,
  initial_n,
  initial_n_pp,
  append = TRUE,
  progress_bar = TRUE,
  ...
)

Arguments

object	Either a MizerParams object or a MizerSim object (which contains a MizerParams object).
effort	The effort of each fishing gear through time. See notes below.
t_max	The number of years the projection runs for. The default value is 100. This argument is ignored if an array is used for the effort argument. See notes below.
dt	Time step of the solver. The default value is 0.1.
t_save	The frequency with which the output is stored. The default value is 1. This argument is ignored if an array is used for the effort argument. See notes below.
t_start	The the year of the start of the simulation. The simulation will cover the period from t_start to t_start + t_max. Defaults to 0. Ignored if an array is used for the effort argument or a MizerSim for the object argument.
initial_n	The initial abundances of species. Instead of using this argument you should set initialN(params) to the desired value.
initial_n_pp	The initial abundances of resource. Instead of using this argument you should set initialNResource(params) to the desired value.
append	A boolean that determines whether the new simulation results are appended to the previous ones. Only relevant if object is a MizerSim object. Default = TRUE.
progress_bar	Either a boolean value to determine whether a progress bar should be shown in the console, or a shiny Progress object to implement a progress bar in a shiny app.
...	Other arguments will be passed to rate functions.

Value

An object of class MizerSim.

Note

The effort argument specifies the level of fishing effort during the simulation. If it is not supplied, the initial effort stored in the params object is used. The effort can be specified in four different ways:

• A single numeric value. This specifies the effort of all fishing gears which is constant through time (i.e. all the gears have the same constant effort).

• A named vector whose names match with existing gear names. The values in the vector specify the constant fishing effort for those fishing gears, i.e. the effort is constant through time. The effort for gears that are not included in the effort vector is set to 0.

• A numerical vector which has the same length as the number of fishing gears. The values in the vector specify the constant fishing effort of each of the fishing gears, with the ordering assumed to be the same as in the MizerParams object.

• A numerical array with dimensions time x gear. This specifies the fishing effort of each gear at each time step. The first dimension, time, must be named numerically and increasing. The second dimension of the array must be named and the names must correspond to the gear names in the MizerParams object. The value for the effort for a particular time is used during the interval from that time to the next time in the array.

If effort is specified as an array then the smallest time in the array is used as the initial time for the simulation. Otherwise the initial time is set to the final time of the previous simulation if object is a MizerSim object or to t_start otherwise. Also, if the effort is an array then the t_max and t_save arguments are ignored and the simulation times will be taken from the effort array.

If the object argument is of class MizerSim then the initial values for the simulation are taken from the final values in the MizerSim object and the corresponding arguments to this function will be ignored.

Examples

params <-  NS_params
# With constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# With constant fishing effort which is different for each gear
effort <- c(Industrial = 0, Pelagic = 1, Beam = 0.5, Otter = 0.5)
sim <- project(params, t_max = 20, effort = effort)
# With fishing effort that varies through time for each gear
gear_names <- c("Industrial","Pelagic","Beam","Otter")
times <- seq(from = 1, to = 10, by = 1)
effort_array <- array(NA, dim = c(length(times), length(gear_names)),
    dimnames = list(time = times, gear = gear_names))
effort_array[,"Industrial"] <- 0.5
effort_array[,"Pelagic"] <- seq(from = 1, to = 2, length = length(times))
effort_array[,"Beam"] <- seq(from = 1, to = 0, length = length(times))
effort_array[,"Otter"] <- seq(from = 1, to = 0.5, length = length(times))
sim <- project(params, effort = effort_array)

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