Get total mortality rate needed to project standard mizer model

Calculates the total mortality rate \(\mu_i(w)\) (in units 1/year) on each species by size from predation mortality, background mortality and fishing mortality. You would not usually call this function directly but instead use getMort(), which then calls this function unless an alternative function has been registered, see below.

Usage

mizerMort(params, n, n_pp, n_other, t, f_mort, 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.)
f_mort: A two dimensional array (species x size) with the fishing mortality
pred_mort: A two dimensional array (species x size) with the predation mortality
...: Unused

Value

A named two dimensional array (species x size) with the total mortality rates.

Details

If your model contains additional components that you added with setComponent() and for which you specified a mort_fun function then the mortality inflicted by these components will be included in the returned value.

Your own mortality function

By default getMort() calls mizerMort(). However you can replace this with your own alternative mortality function. If your function is called "myMort" then you register it in a MizerParams object params with

params <- setRateFunction(params, "Mort", "myMort")

Your function will then be called instead of mizerMort(), with the same arguments.