Get the fishing mortality by time, gear, species and size

Calculates the fishing mortality rate \(F_{g,i,w}\) by gear, species and size and possibly time (in units 1/year).

Usage

getFMortGear(object, ...)

Arguments

object

A MizerParams or MizerSim object.

...

Additional arguments that depend on the class of object.

For a MizerParams object:

effort

The effort for 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.

Value

An array. If the effort argument has a time dimension, or a MizerSim is passed in, the output array has four dimensions (time x gear x species x size). If the effort argument does not have a time dimension (i.e. it is a vector or a single numeric), the output array has three dimensions (gear x species x size).

Note

Here: fishing mortality = catchability x selectivity x effort.

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 the same as in the MizerParams object. If the effort argument is not supplied, its value is taken from the @initial_effort slot in the params 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.

See also

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

Examples

# \donttest{
params <-NS_params
# Get the fishing mortality in initial state
F <- getFMortGear(params, effort = 1)
str(F)
#>  num [1:4, 1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>  - attr(*, "dimnames")=List of 3
#>   ..$ gear: chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"
#>   ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w   : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
# Get the initial fishing mortality when effort is different
# between the four gears:
F <- getFMortGear(params, effort = c(0.5, 1, 1.5, 0.75))
# Get the 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 <- getFMortGear(params, effort = effort)
str(F)
#>  num [1:20, 1:4, 1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>  - attr(*, "dimnames")=List of 4
#>   ..$ time: NULL
#>   ..$ gear: chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"
#>   ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w   : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
# Get the fishing mortality using the effort already held in a MizerSim object.
sim <- project(params, t_max = 20, effort = 0.5)
F <- getFMortGear(sim)
F <- getFMortGear(sim, time_range = c(10, 20))
# }