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