Checks unstructured resource parameters and interaction matrix

Usage

setURParams(
  params,
  UR_interaction = NULL,
  initial_algae_growth = NULL,
  carry_capacity = FALSE,
  algae_capacity = NULL,
  detritus_capacity = NULL,
  sen_decomp = NULL,
  ext_decomp = NULL,
  initial_d_external = NULL
)

Arguments

params: MizerParams object
UR_interaction: Interaction matrix for unstructured resources (species x resource)
initial_algae_growth: The initial growth rate of algae in grams/m^2/year. This value is reset to match consumption in the reefSteady() function so that steady state abundances match given values.
carry_capacity: A boolean value that indicates whether the user wants to implement a carrying capacity for unstructured resources. Default is FALSE
algae_capacity: The carrying capacity of the system for algae biomass in grams per year.
detritus_capacity: The carrying capacity of the system for detritus biomass in grams per year.
sen_decomp: The proportion of decomposing mass from senescence mortality that decomposes to become part of the detritus pool. Defaults to 0.8.
ext_decomp: The proportion of decomposing mass from external mortality that decomposes to become part of the detritus pool. Defaults to 0.2.
initial_d_external: The rate at which detritus biomass sinks from the pelagic zone and becomes part of the detritus pool in grams per year. This value is reset to make up any differences in consumption and production in the reefSteady() function so that steady state abundances match observed values.

Value

setURParams MizerParams object with updated unstructured resource parameters

Adding unstructured resources

 mizerReef supports two resource spectra that are not size- structured.
 Algae are consumed by herbivorous fish, while detritus is consumed by
 herbivorous fish and benthic invertebrates. This function sets the
 interaction matrix for these resources as well as any default
 parameters necessary to structure them.

 The resource interaction matrix \eqn{\theta_{ki}} modifies the
 interaction of each functional group \eqn{i} with each unstructured
 resource \eqn{k} in the model. This can be used for example to allow
 for different diet preferences on each unstructured resource.

 Note that interaction with size structured resources, such as
 plankton, is still set with the resource_interaction column of
 the species parameters dataframe.

Detritus consumption

The rate at which detritivorous consumer groups encounter detrital biomass $E_{i.D}(w)$ is controlled by the parameter $\rho_{D.i}$. It scales with the size of the consumer raised to an allometric exponent $m_{det}$ which is taken to be the same as the scaling exponent of the maximum intake rate for fish consumers.

$$E_{i.D}(w)=\rho_{i.D}\, w^{m_{det}}\,B_D $$

The mass specific consumption rate then accounts for the preference of functional group $i$ for detritus, $\theta_{i.D}$ and the feeding level $f_i(w)$. This gives the mass-specific detritus consumption rate:

$$c_D = \sum_i\int\rho_{i.D}\, w^{m_{det}} N_i(w) \left(1-f_i(w)\right) \theta_{i.D}\,dw$$

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.

Algae consumption

The rate at which herbivorous consumer groups encounter algae biomass $E_{i.A}(w)$ is controlled by the parameter $\rho_{A.i}$. It scales with the size of the consumer raised to an allometric exponent $m_{alg}$ which is taken from empirical data.

$$E_{i.A}(w)=\rho_{i.A}\, w^{m_{alg}}\,B_A$$

The mass specific consumption rate then accounts for the preference of functional group $i$ for algae, $\theta_{i.A}$. This gives the mass-specific algae consumption rate:

$$c_A = \sum_i\int\rho_{i.A}\, w^{m_{alg}} N_i(w)\theta_{i.A}\,dw$$