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 for a single time step.
getMort( params, n = initialN(params), n_pp = initialNResource(params), n_other = initialNOther(params), effort = getInitialEffort(params), t = 0, ... )
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
A numeric vector of the effort by gear or a single numeric effort value which is used for all gears.
The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)
A two dimensional array (prey species x prey size).
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
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
params <- setRateFunction(params, "Mort", "myMort")
Your function will then be called instead of
mizerMort(), with the
Other rate functions: