setMetabolicRate: 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
Value
setMetabolicRate(): A MizerParams object with updated metabolic rate.
getMetabolicRate() or equivalently metab(): An array
(species x size) with the metabolic rate.
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
metabis not given explicitly and if the exponent is not specified in apcolumn in thespecies_params.- reset
![[Experimental]](figures/lifecycle-experimental.svg?package=mizer&version=2.5.3)
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
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()