Detritus production rate — getDetritusProduction • mizerReef

Gives a named vector with the rates at which different components of the ecosystem produce detritus:

Usage

getDetritusProduction(params, n = params@initial_n, rates = getRates(params))

Arguments

params: MizerParams
n: A matrix of current species abundances (species x size)
rates: A list of rates as returned by getRates()

Value

A vector with named entries "feces", "decomp", and "external", giving the rates at which detritus biomass is produced by each of these sources in grams per year.

Details

consumed biomass not assimilated by predators ("feces"),
decomposing dead organisms ("decomp"),
the pelagic zone ("external").

This function returns a vector with the individual contributions for each source. These can be summed with sum() to get the total detritus production rate.

Detritus production

The rate $p_D$ at which detritus biomass is produced by the ecosystem has contributions from three sources:

$$p_D = p_{D.f} + p_{D.d} + p_{D.ext}$$

$p_{D.f}$ comes from the biomass that is consumed but not assimilated and is given by:

$$p_{D.f} = \sum_i(1-\alpha_i)\int E_i(w)\,dw$$

$p_{D.d}$ comes from the biomass of fish that die as a result of external mortality. External mortality includes local deaths that lead to detritus but also deaths due to predation by species that are not explicitly modelled, for example transient predators, mammals, or sea birds. Thus, only a proportion prop_decomp of this material decomposes to detritus. The detritus production from decomposing dead organisms is given by:

$$p_{D.d} = \sum_i\int\mu_{seni.i}(w)N_i(w)w\,dw + \mathtt{prop\_decomp}\, \sum_i\int\mu_{nat.i}(w)N_i(w)w\,dw$$

$p_{D.ext}$ is the rate at which detritus enters the system from unmodelled or external sources. For coral reefs, this includes detritus produced by sponges and coral mucous as well as waste material that sinks in from the pelagic zone. This rate is a model parameter independent of any other model component. It is set so that production and consumption are equal for the chosen steady state abundances.