mizer (version 3.0.0)

getFMort: Get the total fishing mortality rate from all fishing gears by time, species and size.

Description

Calculates the total fishing mortality (in units 1/year) from all gears by species and size and possibly time. See setFishing() for details of how fishing gears are set up.

Usage

getFMort(object, ...)

Value

• MizerParams with vector effort: An ArraySpeciesBySize object (species x size) with the fishing mortality rates.

• MizerParams with time-dimensioned effort or MizerSim: An ArrayTimeBySpeciesBySize object (time x species x size).

The effort argument is only used if a MizerParams object is passed in. The effort argument can be a two dimensional array (time x gear), a vector of length equal to the number of gears (each gear has a different effort that is constant in time), or a single numeric value (each gear has the same effort that is constant in time). The order of gears in the effort argument must be the same as in the MizerParams

object.

If the object argument is of class MizerSim then the effort slot of the MizerSim object is used and the effort argument is not used.

Arguments

object

A MizerParams or MizerSim object.

...

Additional arguments that depend on the class of object.

For a MizerParams object:

effort

The effort of each fishing gear. See notes below. Defaults to the initial effort stored in object.

n

A matrix of species abundances (species x size). Defaults to the initial abundances stored in object.

n_pp

A vector of the resource abundance by size. Defaults to the initial resource abundance stored in object.

n_other

A named list of the abundances of other dynamical components. Defaults to the initial values stored in object.

t

The time for which to do the calculation. Defaults to 0.

For a MizerSim object:

time_range

Subset the returned fishing mortalities by time. The time range is either a vector of values, a vector of min and max time, or a single value. Defaults to the whole time range of the simulation.

drop

Should dimensions of length 1 be dropped, e.g. if your community only has one species it might make presentation of results easier. Defaults to TRUE.

Your own fishing mortality function

By default getFMort() calls mizerFMort(). However you can replace this with your own alternative fishing mortality function. If your function is called "myFMort" then you register it in a MizerParams object params with

params <- setRateFunction(params, "FMort", "myFMort")

Your function will then be called instead of mizerFMort(), with the same arguments.

Details

The total fishing mortality is just the sum of the fishing mortalities imposed by each gear, \(F_i(w)=\sum_g F_{g,i,w}\). The fishing mortality for each gear is obtained as catchability x selectivity x effort.

See Also

Other rate functions: getDiffusion(), getEGrowth(), getERepro(), getEReproAndGrowth(), getEncounter(), getFMortGear(), getFeedingLevel(), getFlux(), getMort(), getPredMort(), getPredRate(), getRDD(), getRDI(), getRates(), getResourceMort()

Examples

# \donttest{
params <- NS_params
# Get the total fishing mortality in the initial state
F <- getFMort(params, effort = 1)
str(F)
# Get the initial total fishing mortality when effort is different
# between the four gears:
F <- getFMort(params, effort = c(0.5,1,1.5,0.75))
# Get the total fishing mortality when effort is different
# between the four gears and changes with time:
effort <- array(NA, dim = c(20,4))
effort[, 1] <- seq(from = 0, to = 1, length = 20)
effort[, 2] <- seq(from = 1, to = 0.5, length = 20)
effort[, 3] <- seq(from = 1, to = 2, length = 20)
effort[, 4] <- seq(from = 2, to = 1, length = 20)
F <- getFMort(params, effort = effort)
str(F)
# Get the total fishing mortality using the effort already held in a
# MizerSim object.
sim <- project(params, t_max = 20, effort = 0.5)
F <- getFMort(sim)
F <- getFMort(sim, time_range = c(10, 20))
# }