getFMort: Get the total fishing mortality rate from all fishing gears...

In drfinlayscott/mizer: Dynamic Multi-Species Size Spectrum Modelling

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, effort, time_range, drop = TRUE)

Arguments

object	A MizerParams object or a MizerSim object
effort	The effort of each fishing gear. Only used if the object argument is of class MizerParams. 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 object argument is of type MizerSim.
drop	Only used when object is of type MizerSim. Should dimensions of length 1 be dropped, e.g. if your community only has one species it might make presentation of results easier. Default is TRUE.

Details

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

Value

An array. If the effort argument has a time dimension, or object is of class MizerSim, the output array has three dimensions (time x species x size). If the effort argument does not have a time dimension, the output array has two dimensions (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.

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.

See Also

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

Examples

params <- NS_params
# Get the total fishing mortality when effort is constant for all 
# gears and time:
getFMort(params, effort = 1)
# Get the total fishing mortality when effort is different
# between the four gears but constant in time:
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)
getFMort(params, effort = effort)
# Get the total fishing mortality using the effort already held in a 
# MizerSim object.
sim <- project(params, t_max = 20, effort = 0.5)
getFMort(sim)
getFMort(sim, time_range = c(10, 20))

drfinlayscott/mizer documentation built on April 13, 2024, 9:16 a.m.