setMetabolicRate: Set metabolic rate

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Set metabolic rate

Description

Sets the rate at which energy is used for metabolism and activity. You will usually not need to call this function directly. Instead change the k, ks and p species parameters with ⁠given_species_params(params) <-⁠ and let mizer recalculate the metabolic rate for you. Call setMetabolicRate() directly only if you want to impose a different functional form for the size dependence of the metabolic rate. See vignette("guide-change-parameters") for a full explanation of when to reach for which level of the model.

Usage

setMetabolicRate(object, metab = NULL, p = deprecated(), reset = FALSE, ...)

metab(params)

metab(params) <- value

Arguments

object	A MizerParams object
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. Set the p column in the species parameters instead, with species_params(params)$p <- value. This argument never took effect on a MizerParams object because such an object always has a p column already, and the argument was only used to fill in a missing one.
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
params	A MizerParams object
value	metab

Value

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

metab(): An ArraySpeciesBySize object (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.

If the metab slot has a comment and reset = FALSE, then a recalculation from the species parameters is suppressed and a message is issued if the recalculated values would differ from the stored ones.

See Also

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

Examples

# Inspect the current metabolic rate
metab(NS_params)["Cod", 1:5]

# Reset metabolic rate from species parameters
params <- setMetabolicRate(NS_params, reset = TRUE)
metab(params)["Cod", 1:5]

mizer documentation built on Aug. 24, 2026, 9:08 a.m.