mizer (version 2.2.1)

setExtMort: Set external mortality rate

Description

Set external mortality rate

Usage

setExtMort(
  params,
  z0 = NULL,
  z0pre = 0.6,
  z0exp = -1/4,
  comment_z0 = "set manually",
  ...
)
getExtMort(params)

Arguments

params

MizerParams

z0

Optional. An array (species x size) holding the external mortality rate.

z0pre

If z0, the mortality from other sources, is not a column in the species data frame, it is calculated as z0pre * w_inf ^ z0exp. Default value is 0.6.

z0exp

If z0, the mortality from other sources, is not a column in the species data frame, it is calculated as z0pre * w_inf ^ z0exp. Default value is n-1.

comment_z0

A string describing how the value for 'z0' was obtained. This is ignored if 'z0' is not supplied or already has a comment attribute.

...

Unused

Value

MizerParams object with updated external mortality rate. Because of the way the R language works, setExtMort() does not make the changes to the params object that you pass to it but instead returns a new params object. So to affect the change you call the function in the form params <- setExtMort(params, ...).

Setting external mortality rate

The external mortality is all the mortality that is not due to fishing or predation by predators included in the model. The external mortality could be due to predation by predators that are not explicitly included in the model (e.g. mammals or seabirds) or due to other causes like illness. It is a rate with units 1/year.

The z0 argument allows you to specify an external mortality rate that depends on species and body size. You can see an example of this in the Examples section of the help page for setExtMort().

If the z0 argument is not supplied, then the external mortality is assumed to depend only on the species, not on the size of the individual: \(\mu_{b.i}(w) = z_{0.i}\). The value of the constant \(z_0\) for each species is taken from the z0 column of the species_params data frame, if that column exists. Otherwise it is calculated as $$z_{0.i} = {\tt z0pre}_i\, w_{inf}^{\tt z0exp}.$$

See Also

Other functions for setting parameters: gear_params(), resource_params(), setFishing(), setInitialValues(), setInteraction(), setMaxIntakeRate(), setMetabolicRate(), setParams(), setPredKernel(), setReproduction(), setResource(), setSearchVolume(), species_params()

Examples

# NOT RUN {
params <- newMultispeciesParams(NS_species_params)

#### Setting allometric death rate #######################

# Set coefficient for each species. Here we choose 0.1 for each species
z0pre <- rep(0.1, nrow(species_params(params)))

# Multiply by power of size with exponent, here chosen to be -1/4
# The outer() function makes it an array species x size
z0 <- outer(z0pre, w(params)^(-1/4))

# Change the external mortality rate in the params object
params <- setExtMort(params, z0 = z0)
# }