setMetabolicRate {mizer}

Set metabolic rate

Description

Sets the rate at which energy is used for metabolism and activity

Usage

setMetabolicRate(params, metab = NULL, p = NULL, reset = FALSE, ...)

getMetabolicRate(params)

metab(params)

metab(params) <- value

Arguments

params

MizerParams

metab

Optional. An array (species x size) holding the metabolic rate for each species at size. If not supplied, a default is set as described in the section "Setting metabolic rate".

p

The allometric metabolic exponent. This is only used if metab is not given explicitly and if the exponent is not specified in a p column in the species_params.

reset

If set to TRUE, then the metabolic rate will be reset to the value calculated from the species parameters, even if it was previously overwritten with a custom value. If set to FALSE (default) then a recalculation from the species parameters will take place only if no custom value has been set.

...

Unused

value

metab

Value

setMetabolicRate(): A MizerParams object with updated metabolic rate.

getMetabolicRate() or equivalently metab(): An array (species x size) with the metabolic rate.

Setting metabolic rate

The metabolic rate is subtracted from the energy income rate to calculate the rate at which energy is available for growth and reproduction, see getEReproAndGrowth(). It is measured in grams/year.

If the metab argument is not supplied, then for each species the metabolic rate k(w) for an individual of size w is set to

k(w) = k_s w^p + k w,

where k_s w^p represents the rate of standard metabolism and k w is the rate at which energy is expended on activity and movement. The values of k_s, p and k are taken from the ks, p and k columns in the species parameter dataframe. If any of these parameters are not supplied, the defaults are k = 0, p = n and

k_s = f_c h \alpha w_{mat}^{n-p},

where f_c is the critical feeding level taken from the fc column in the species parameter data frame. If the critical feeding level is not specified, a default of f_c = 0.2 is used.

See Also

Other functions for setting parameters: gear_params(), setExtEncounter(), setExtMort(), setFishing(), setInitialValues(), setInteraction(), setMaxIntakeRate(), setParams(), setPredKernel(), setReproduction(), setSearchVolume(), species_params()