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

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

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

Description

Calculates the fishing mortality by gear, species and size at each time step in the effort argument. Used by the project_therMizer method to perform simulations.

getFMortGear method for therMizerParams object with constant effort.

getFMortGear method for therMizerParams object with time changing effort.

getFMortGear method for therMizerSim object.

Usage

getFMortGear(object, effort, ...)

## S4 method for signature 'therMizerParams,numeric'
getFMortGear(object, effort, ...)

## S4 method for signature 'therMizerParams,matrix'
getFMortGear(object, effort, ...)

## S4 method for signature 'therMizerSim,missing'
getFMortGear(object, effort,
  time_range = dimnames(object@effort)$time, ...)

Arguments

object	A therMizerParams object or a therMizerSim object.
effort	The effort of each fishing gear. Only needed if the object argument is of class therMizerParams. See notes below.
...	Other arguments (currently unused).
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 object argument is of type therMizerSim.

Value

An array. If the effort argument has a time dimension, or a therMizerSim 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 therMizerParams 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 therMizerParams object.

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

Examples

## Not run: 
data(NS_species_params_gears)
data(inter)
params <- therMizerParams(NS_species_params_gears, inter)
# Get the fishing mortality when effort is constant
# for all gears and time:
getFMortGear(params, effort = 1)
# Get the fishing mortality when effort is different
# between the four gears but constant in time:
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)
getFMortGear(params, effort=effort)
# Get the fishing mortality using the effort already held in a therMizerSim object.
sim <- project_therMizer(params, t_max = 20, effort = 0.5)
getFMortGear(sim)
getFMortGear(sim, time_range=c(10,20))

## End(Not run)

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