project_therMizer: project_therMizer method for the size based modelling

In pwoodworth-jefcoats/Size-Based-Modeling: Mizer With The Effects Of Temperature Included

project_therMizer method for the size based modelling

Description

Runs the size-based model simulation and projects the size based model through time. project_therMizer is called using an object of type therMizerParams, an object that contains the effort of the fishing gears through time, and an object that contains the ocean temperature in each realm through time. The method returns an object of type therMizerSim which can then be explored with a range of summary and plotting methods.

Project without an effort or ocean_temp argument.

Project with a constant effort and ocean_temp.

Project with time varying effort and ocean temperature

Usage

project_therMizer(object, effort, ocean_temp, n_plank, ...)

## S4 method for signature 'therMizerParams,missing,missing,missing'
project_therMizer(object,
  effort, ocean_temp, n_plank, ...)

## S4 method for signature 'therMizerParams,numeric,numeric,numeric'
project_therMizer(object,
  effort, ocean_temp, n_plank, t_max = 100, dt = 0.1, ...)

## S4 method for signature 'therMizerParams,array,array,array'
project_therMizer(object, effort,
  ocean_temp, n_plank, t_save = 1, dt = 0.1,
  initial_n = get_initial_n(object), initial_n_pp = object@cc_pp, ...)

Arguments

object	A therMizerParams object
effort	The effort of each fishing gear through time. See notes below.
ocean_temp	The ocean temperature in each oceanic realm through time. See notes below.
n_plank	The log10 abundance-at-size for the plankton community. Has the dimensions of time step (or constant) x size.
...	Currently unused.
t_max	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 effort argument, in which case this argument is ignored. 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.
initial_n	The initial populations of the species. See the notes below.
initial_n_pp	The initial population of the background spectrum. It should be a numeric vector of the same length as the w_full slot of the therMizerParams argument. By default the cc_pp slot of the therMizerParams argument is used.

Value

An object of type therMizerSim.

Note

The 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 therMizerParams 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 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 therMizerParams argument.

If effort is specified as an array then the t_max argument is ignored and the maximum simulation time is the taken from the dimension names.

The ocean_temp argument specifies the ocean temperature during the simulation. It can be specified in three different ways:

• A single numeric value. This specifies the temperature in all realms which is constant through time (i.e., all realms have the same constant temperature).

• A numerical vector which has the same length as the number of realms. The vector must be named and the names must correspond to the realm names in the therMizerParams object. The values in the vectory specify the constant temperature for each of the realms, i.e., the temperature is constant through time but each realm may have a different temperature.

• A numerical array with dimensions time step x realm. This specifies the temperature in each realm at each time step. The first dimenions, time, must be named numerically and contiguously. The second dimension of the array must be named and the names must correspond to the realm names in the therMizerParams argument.

If ocean_temp is specified as an array then the t_max argument is ignored and the maximum simulation time is taken from the dimension names

The initial_n argument is a matrix with dimensions species x size. The order of species must be the same as in the therMizerParams 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.

See Also

therMizerParams

Examples

## Not run: 
# Data set with different fishing gears
data(NS_species_params_gears)
data(inter)
params <- therMizerParams(NS_species_params_gears, inter)
# With constant fishing effort for all gears for 20 time steps
sim <- project_therMizer(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_therMizer(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_therMizer(params, effort = effort_array)

## End(Not run)

pwoodworth-jefcoats/Size-Based-Modeling documentation built on Sept. 15, 2023, 8:13 a.m.