Expanding external mortality rate to include senescence

Usage

reefSenMort(params, n, n_pp, n_other, t, ...)

Arguments

params: A MizerParams object
n: A matrix of species abundances (species x size).
n_pp: A vector of the resource abundance by size
n_other: A list of abundances for other dynamical components of the ecosystem
t: The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)
...: Unused

Value

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

Senescence mortality

 Senescence mortality \eqn{\mu_{sen.i}(w)} is used to represent
 mortality caused by external sources such as illness or age. This is
 addition to external mortality, \eqn{\mu_{ext.i}(w)}, which represents
 all mortality that is not due to fishing or predation by predators
 included in the model. The rate of senescence mortality is given by:

 \deqn{\mu_{sen.i}(w) = k_{sen}\left(\frac{w}{w_{max.i}}\right)^{p_{sen}}}
      {\mu_{sen.i}(w) = k_{sen} (w/w_{max.i})^{p_{sen}}

 where \eqn{k_{sen}} and \eqn{p_sen} are constants defining the shape
 of the senescence curve and \eqn{w_max.i} is the maximum size
 of species \eqn{i} in grams.

 Users can change all constants with the `setSenMortParams()` function.