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 and plotting_functions.
project( object, effort, t_max = 100, dt = 0.1, t_save = 1, t_start = 0, initial_n, initial_n_pp, initial_n_other, append = TRUE, progress_bar = TRUE, ... )
| object | Either a MizerParams object or a
MizerSim object (which contains a |
|---|---|
| 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. However, this argument is ignored if an array is used for the
|
| 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. Must be an integer multiple of dt. |
| t_start | The the year of the start of the simulation. The simulation
will cover the period from |
| initial_n | The initial abundances of species. A matrix with dimensions
species x size. The order of species must be the same as in the
|
| initial_n_pp | The initial abundances of plankton. A numeric vector.
Ignored if the |
| initial_n_other | The initial abundances of the other dynamical
ecosystem components. It should be a named list with one entry for each
component. Ignored if the |
| append | A boolean that determines whether the new simulation results
are appended to the previous ones. Only relevant if |
| progress_bar | Either a boolean value to determine whether a progress bar should be shown in the console of a shiny progress object to implement a progress bar in a shiny app |
| ... | Currently unused. |
An object of class MizerSim.
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 three 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 numerical vector which has the same length as the number of fishing
gears. The vector must be named and the names must correspond to the gear
names in the MizerParams object. The values in the vector specify the
constant fishing effort of each of the fishing gears, i.e. the effort is
constant through time but each gear may have a different fishing effort.
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 contiguously. The second dimension of the array
must be named and the names must correspond to the gear names in the
MizerParams argument. 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 argument is ignored and the maximum simulation
time is the largest time of 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.
if (FALSE) { # Data set with different fishing gears data(NS_species_params_gears) data(inter) params <- newMultispeciesParams(NS_species_params_gears, inter) # 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) }