Get the fishing mortality by time, gear, species and size
Source:R/rate_functions.R
getFMortGear.RdCalculates the fishing mortality rate \(F_{g,i,w}\) by gear, species and size and possibly time (in units 1/year).
Arguments
- object
A
MizerParamsobject or aMizerSimobject.- effort
The effort for each fishing gear. See notes below.
- 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. Default is the whole time range. Only used if the
objectargument is of typeMizerSim.
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:
getEGrowth(),
getERepro(),
getEReproAndGrowth(),
getEncounter(),
getFMort(),
getFeedingLevel(),
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))
# }