Set the parameters for external mortality
Value
A MizerParams object with updated external mortality parameters
(stored in other_params$ext_mort_params).
External mortality in mizerReef
External mortality in mizerReef includes residual natural mortality
and senescence mortality, representing background sources of death
not explicitly modeled (e.g., predation, disease, aging). This function
allows you to set or override the default rates and scaling for these
processes.
Residual natural mortality is modeled as an allometric function of body
size, decreasing with increasing size. Senescence mortality is modeled
as a power function of relative size, allowing flexible control over
the rate and scaling of age-related death.
If no parameters are provided, defaults are used: nat_mort = 0.2,
sen_prop = 0.1, sen_curve = 0.3. All parameters must be numeric
and non-negative. The function checks for required columns and
valid values if a custom parameter set is provided.Residual natural mortality
Residual natural mortality accounts for any external predation or
fishing mortality that is not explicitly included in the model. It is
assumed to decrease allometrically with body size. Residual natural
mortality is a rate with units 1/year given by:
\deqn{\mu_{nat.i}(w) = \mu_{nat}\, w^{1-n}.}
{\mu_{nat.i}(w) = \mu_{nat}\, w^{1-n}.}
Here \eqn{\mu_{nat}} is the residual natural mortality rate at size
1 g and \eqn{n} is the allometric scaling exponent. In mizerReef,
these default to \eqn{\mu_{nat} = 0.2} and \eqn{n = 0.75}.Senescence mortality
Senescence mortality \eqn{\mu_{sen.i}(w)} is used to represent
mortality caused by background sources such as illness or age. The
rate of senescence mortality (in 1/year) is given by:
\deqn{\mu_{sen.i}(w) = \mathtt{sen\_prop}\,
\left[\max\left(0,\;
\frac{\log_{10}(w)}{\log_{10}(w_{max.i})}
\right)\right]^{\mathtt{sen\_curve}}}{
\mu_{sen.i}(w) = sen_prop *
max(0, log10(w)/log10(w_{max.i}))^sen_curve}
where \eqn{\mathtt{sen\_curve}} is the exponent shaping the
senescence curve and \eqn{\mathtt{sen\_prop}} is the rate the curve
approaches as \eqn{w \to w_{max.i}} (where the ratio is exactly 1).
The ratio is floored at zero before being raised to the
\eqn{\mathtt{sen\_curve}} power, since it is negative for individuals
below 1 gram (where \eqn{\log_{10}(w) < 0}), which would otherwise
raise a negative number to a fractional power -- those individuals
get exactly zero senescence mortality.