setExtMort: Set external mortality rate

Description

Set external mortality rate

Usage

setExtMort(
  params,
  ext_mort = NULL,
  z0pre = 0.6,
  z0exp = -1/4,
  reset = FALSE,
  z0 = deprecated(),
  ...
)
getExtMort(params)
ext_mort(params)
ext_mort(params) <- value

Value

setExtMort(): A MizerParams object with updated external mortality rate.

getExtMort() or equivalently ext_mort(): An array (species x size) with the external mortality.

Arguments

params: MizerParams
ext_mort: Optional. An array (species x size) holding the external mortality rate. If not supplied, a default is set as described in the section "Setting 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_max ^ 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_max ^ z0exp. Default value is n-1.
reset: If set to TRUE, then the external mortality rate will be reset to the value calculated from the z0 parameters, even if it was previously overwritten with a custom value. If set to FALSE (default) then a recalculation from the species parameters will take place only if no custom value has been set.
z0: Use ext_mort instead. Not to be confused with the species_parameter z0.
...: Unused
value: ext_mort

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

Examples

Run this code

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
allo_mort <- outer(z0pre, w(params)^(-1/4))

# Change the external mortality rate in the params object
ext_mort(params) <- allo_mort