Set the parameters for external mortality

mizerReef models contain two sources of external mortality, residual natural mortality and senescence. This function checks if given parameters are valid, sets defaults, and then stores them in the mizerParams object.

Usage

setExtMortParams(params, ext_mort_params = NULL)

Arguments

params

MizerParams object

Optional parameters:

ext_mort_params

Named list containing desired mortality parameters

Value

MizerParams object with updated mortality parameters

Details

External mortality is implemented by default in mizerReef. You do not need to set these parameters. This function should only be used to change default values.

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) = k_{sen}\left(
                             \frac{log_{10}(w)}{log_{10}(w_{max.i})}
                             \right)^{p_{sen}}}
      {\mu_{sen.i}(w) = k_{sen}
      (log_{10}(w)/log_{10}(w_{max.i}))^{p_{sen}}}

 where \eqn{k_{sen}} is the rate of senescence mortality, \eqn{p_sen}
 defines the slope of the senescence curve, \eqn{w_max.i} maximum body
 size of group \eqn{i} in grams.