Get the total fishing mortality rate from all fishing gears

Calculates the total fishing mortality (in units 1/year) from all gears by species and size. The total fishing mortality is just the sum of the fishing mortalities imposed by each gear, \(\mu_{f.i}(w)=\sum_g F_{g,i,w}\). You would not usually call this function directly but instead use getFMort(), which then calls this function unless an alternative function has been registered, see below.

Usage

mizerFMort(params, n, n_pp, n_other, t, effort, e_growth, pred_mort, ...)

Arguments

params: A MizerParams object
n: A matrix of species abundances (species x size).
n_pp: A vector of the resource abundance by size
n_other: A list of abundances for other dynamical components of the ecosystem
t: The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)
effort: A vector with the effort for each fishing gear.
e_growth: An array (species x size) with the energy available for growth as calculated by getEGrowth(). Unused.
pred_mort: A two dimensional array (species x size) with the predation mortality as calculated by getPredMort(). Unused.
...: Unused

Value

An array (species x size) with the fishing mortality.

Note

Here: fishing mortality = catchability x selectivity x effort.

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.