getRates: Get all rates

In drfinlayscott/mizer: Dynamic Multi-Species Size Spectrum Modelling

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.

Value

List of rates.

See Also

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

Examples

rates <- getRates(NS_params)
names(rates)
identical(rates$encounter, getEncounter(NS_params))

drfinlayscott/mizer documentation built on April 13, 2024, 9:16 a.m.