Get the size specific senescence mortality rate

Returns the rate of senescence mortality at each size by functional group.

Usage

getSenMort(
  params,
  n = initialN(params),
  n_pp = params@initial_n_pp,
  n_other = initialNOther(params),
  t = 0,
  ...
)

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.

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.