project method for the size based modelling
Runs the size-based model simulation and projects the
size based model through time.
project is called
using an object of type
MizerParams and an object
that contains the effort of the fishing gears through
time. The method returns an object of type
MizerSim which can then be explored with a
range of summary and plotting methods.
The effort of each fishing gear through time. See notes below.
The maximum time the projection runs for.
The default value is 100. However, this argument is not
needed if an array is used for the
Time step of the solver. The default value is 0.1.
The frequency with which the output is stored. The default value is 1.
The initial populations of the species. See the notes below.
The initial population of the
background spectrum. It should be a numeric vector of the
same length as the
An object of type of
An object of type
effort argument specifies the level of fishing
effort during the simulation. It 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
MizerParamsobject. 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 step 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
If effort is specified as an array then the
argument is ignored and the maximum simulation time is
the taken from the dimension names.
initial_n argument is a matrix with dimensions
species x size. The order of species must be the same as
MizerParams argument. If the initial
population is not specified, the argument is set by
default by the
get_initial_n function which is set
up for a North Sea model.
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## Not run: # Data set with different fishing gears data(NS_species_params_gears) data(inter) params <- MizerParams(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) ## End(Not run)