Expanding external mortality rate to include senescence

Senescence mortality represents mortality caused by background sources such as illness or age, in addition to residual natural mortality (see setExtMortParams()'s "Residual natural mortality" section), which represents all other mortality that is not due to fishing or predation by predators included in the model.

Usage

reefSenMort(params, ...)

Arguments

params

A MizerParams object

...

Unused

Value

A named two dimensional array (species x size) with the senescence mortality rates.

Details

Users can change sen_prop/sen_curve via setExtMortParams().

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.