mizer (version 2.0.0)

getMort: Get total mortality rate

Description

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.

Usage

getMort(
  params,
  n = initialN(params),
  n_pp = initialNResource(params),
  n_other = initialNOther(params),
  effort = getInitialEffort(params),
  f_mort = getFMort(params, effort),
  pred_mort = getPredMort(params, n = n, n_pp = n_pp, n_other = n_other)
)

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

effort

A numeric vector of the effort by gear or a single numeric effort value which is used for all gears.

f_mort

A two dimensional array (species x size) of fishing mortality (optional).If not supplied is calculated using the getFMort() function.

pred_mort

A two dimensional array of predation mortality (optional). Has dimensions no. sp x no. size bins in the community. If not supplied is calculated using the getPredMort() function.

Value

A two dimensional array (prey species x prey size).

See Also

getPredMort(), getFMort()

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

Examples

# NOT RUN {
params <- newMultispeciesParams(NS_species_params_gears, inter)
# Project with constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get the total mortality at a particular time step
getMort(params,sim@n[21,,],sim@n_pp[21,],effort=0.5)
# }