setMaxIntakeRate: Set maximum intake rate

Description

You will usually not need to call this function directly. Instead change the h and n species parameters with given_species_params(params) <- and let mizer recalculate the maximum intake rate for you. Call setMaxIntakeRate() directly only if you want to impose a different functional form for the size dependence of the intake rate. See vignette("guide-change-parameters") for a full explanation of when to reach for which level of the model.

Usage

setMaxIntakeRate(params, intake_max = NULL, reset = FALSE, ...)
intake_max(params)
intake_max(params) <- value

Value

setMaxIntakeRate(): A MizerParams object with updated maximum intake rate.

intake_max(): An ArraySpeciesBySize object (species x size) with the maximum intake rate.

Arguments

params: MizerParams
intake_max: Optional. An array (species x size) holding the maximum intake rate for each species at size. If not supplied, a default is set as described in the section "Setting maximum intake rate".
reset: If set to TRUE, then the intake 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: intake_max

Setting maximum intake rate

The maximum intake rate $h_i(w)$ of an individual of species $i$ and weight $w$ determines the feeding level, calculated with getFeedingLevel(). It is measured in grams/year.

If the intake_max argument is not supplied, then the maximum intake rate is set to $$h_i(w) = h_i w^{n_i}.$$ The values of $h_i$ (the maximum intake rate of an individual of size 1 gram) and $n_i$ (the allometric exponent for the intake rate) are taken from the h and n columns in the species parameter dataframe. If the h column is not supplied in the species parameter dataframe, it is calculated by the get_h_default() function. If the n column is not supplied, a default of $n_i = 3/4$ is used.

If $h_i$ is set to Inf, fish of species i will consume all encountered food.

If the intake_max 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.

Examples

Run this code

# Inspect the current maximum intake rate
intake_max(NS_params)["Cod", 1:5]

# Increase intake rate for Cod by 50%
im <- intake_max(NS_params)
im["Cod", ] <- im["Cod", ] * 1.5
params <- setMaxIntakeRate(NS_params, intake_max = im)
intake_max(params)["Cod", 1:5]