setExtMort: Set external mortality rate

Description

You will usually not need to call this function directly. Instead change the z0, z_ext and d species parameters with given_species_params(params) <- and let mizer recalculate the external mortality rate for you. Call setExtMort() directly only if you want to impose a different functional form for the size dependence of the external mortality. See vignette("guide-change-parameters") for a full explanation of when to reach for which level of the model.

Usage

setExtMort(
  params,
  ext_mort = NULL,
  z0pre = 0.6,
  z0exp = params@resource_params$n - 1,
  reset = FALSE,
  z0 = deprecated(),
  ...
)
ext_mort(params)
ext_mort(params) <- value

Value

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

ext_mort(): An ArraySpeciesBySize object (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 present in given_species_params(), it is calculated as z0pre * w_inf ^ z0exp. Default value is 0.6.
z0exp: The exponent used with z0pre to calculate non-given z0. Default value is n - 1.
reset: If set to TRUE, then the external mortality rate will be reset to the value calculated from the species 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 taken from the species parameters as $$\mu_{ext.i}(w) = z_{0.i} + z_{ext.i} w^{d_i}.$$ The value of the constant $z_0$ for each species is taken from the z0 column of given_species_params() if it is present there. Otherwise it is recalculated, even if a value from an earlier calculation is still present in species_params, as $$z_{0.i} = {\tt z0pre}_i\, w_{inf}^{\tt z0exp}.$$ When z0pre or z0exp is supplied explicitly and used to calculate non-given z0, the resulting values are recorded in given_species_params(). Values calculated from the defaults z0pre = 0.6 and z0exp = n - 1 are not recorded there. If either argument is supplied but cannot be used because z0 is given for every species or because ext_mort was supplied, a warning is issued. Missing values of z_ext are set to 0 and missing values of d are set to n - 1.

By default the power law is evaluated at the left bin edges $w_j$ (point sampling). If the bin_average entry of the second_order_w slot is TRUE (see second_order_w()), then the $z_{ext} w^d$ term is instead replaced by its exact average over each bin $[w_j, w_{j+1}]$, $$\frac{z_{ext}}{\Delta w_j}\int_{w_j}^{w_{j+1}} w^d\, dw = z_{ext}\,\frac{w_{j+1}^{d+1} - w_j^{d+1}}{(d+1)\,\Delta w_j},$$ (with the limiting form $z_{ext}\ln(w_{j+1}/w_j)/\Delta w_j$ when $d = -1$). This is the consistent choice in the finite-volume scheme, where the external mortality multiplies the bin-averaged abundance. The bin-averaging is applied only to the auto-calculated power-law default; a user-supplied ext_mort array is left untouched.

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