mizer (version 2.3.0)

getRates: Get all rates

Description

Calls other rate functions in sequence and collects the results in a list.

Usage

getRates(
  params,
  n = initialN(params),
  n_pp = initialNResource(params),
  n_other = initialNOther(params),
  effort,
  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

effort

The effort for each fishing gear

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

Details

By default this function returns a list with the following components:

• encounter from mizerEncounter()

• feeding_level from mizerFeedingLevel()

• e from mizerEReproAndGrowth()

• e_repro from mizerERepro()

• e_growth from mizerEGrowth()

• pred_rate from mizerPredRate()

• pred_mort from mizerPredMort()

• f_mort from mizerFMort()

• mort from mizerMort()

• rdi from mizerRDI()

• rdd from BevertonHoltRDD()

• resource_mort from mizerResourceMort()

However you can replace any of these rate functions by your own rate function if you wish, see setRateFunction() for details.

See Also

Other rate functions: getEGrowth(), getEReproAndGrowth(), getERepro(), getEncounter(), getFMortGear(), getFMort(), getFeedingLevel(), getMort(), getPredMort(), getPredRate(), getRDD(), getRDI(), getResourceMort()

Examples

# NOT RUN {
rates <- getRates(NS_params)
names(rates)
identical(rates$encounter, getEncounter(NS_params))
# }