Set detritus parameters for mizerReef

Usage

setDetritusParams(
  params,
  detritus_capacity = NULL,
  sen_decomp = NULL,
  ext_decomp = NULL,
  external = NULL,
  UR_interaction = NULL,
  use_UR_cc = FALSE,
  detritus_colour = "plum4"
)

Arguments

params: A MizerParams object.
detritus_capacity: Numeric. Carrying capacity for detritus biomass in grams per year. Default is 1.
sen_decomp: Numeric. Proportion of decomposing mass from senescence mortality that becomes detritus. Default is 0.8.
ext_decomp: Numeric. Proportion of decomposing mass from external mortality that becomes detritus. Default is 0.2.
external: Numeric. Rate at which detritus biomass sinks from the pelagic zone (grams per year). Default is 1.
UR_interaction: Optional. A named list or array with one or more resource interaction vectors (e.g. interaction_algae, interaction_detritus, interaction_sponge), each of length equal to the number of species. If NULL, will use columns in species_params or set to zero. All values must be numeric and between 0 and 1.
use_UR_cc: Logical. Whether to implement a carrying capacity for detritus. Default is FALSE. This flag is stored in the other_params slot.
detritus_colour: Character. Colour to use for detritus in plots. Default is "plum4".

Value

A MizerParams object with updated detritus parameters (in other_params$detritus).

Details

All detritus-related parameters (capacity, decomposition rates, external input) are stored in the detritus component of other_params (i.e. other_params(params)$detritus), the same location mizer::getComponent()/mizer::removeComponent() use. Resource interaction strengths are set in the species_params data frame. This function supports flexible multi-resource interaction via the UR_interaction argument.

Detritus as an unstructured resource

 Detritus in mizerReef is modeled as a non-size-structured resource
 produced by the decomposition of organic materials. Detritus is consumed
 by detritivores and benthic invertebrates. This function sets the
 carrying capacity, decomposition proportions, and interaction strengths
 for detritus, supporting flexible diet preferences.

 The interaction strength (\eqn{\theta_{i,detritus}}) for each species \eqn{i}
 determines how strongly that group feeds on detritus. This can be set via the
 `interaction_detritus` column in the species parameter data frame, or directly
 via the `UR_interaction` argument. If neither is provided, all interaction
 strengths are set to zero and a warning is issued.

 The carrying capacity (`detritus_capacity`) limits the maximum standing
 stock of detritus.

 The proportions of decomposing mass from senescence (`sen_decomp`) and
 external mortality (`ext_decomp`) that become detritus are set here,
 with typical defaults of 0.8 and 0.2, respectively. The rate at which
 detritus sinks from the pelagic zone (`d_external_initial`) is also set,
 controlling detritus input from external sources. These values may be
 reset by [reefSteady()] to ensure steady state abundances match observed
 or target values.

 Carrying capacity can be toggled with `use_UR_cc`. When enabled, detritus
 biomass will be limited by the specified capacity.

 Note: Interaction with size-structured resources, such as plankton, is
 set with the resource_interaction column of the species parameters dataframe.

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:

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

where $f_i(w)$ is the feeding level (see algae_consumption()'s "Algae consumption" section for how satiation controls it), so that $(1-f_i(w))\,E_i(w)$ is the biomass actually consumed (as opposed to merely encountered) – unlike algae consumption, which deliberately ignores feeding level (see algae_consumption()), detritus's egestion term uses the same feeding-level-adjusted consumption rate as getDetritusConsumption() and detritus_consumption().

$p_{D.d}$ comes from the biomass of fish that die, combining two mortality sources that each decompose to detritus at their own rate: senescence mortality (see getSenMort()) and external mortality, i.e. local deaths that lead directly to detritus as well as deaths due to predation by species that are not explicitly modelled, for example transient predators, mammals, or sea birds. Only a proportion of each source's dead biomass decomposes to detritus, set independently by sen_decomp (senescence, default 0.8) and ext_decomp (external mortality, default 0.2; see setDetritusParams()). The detritus production from decomposing dead organisms is given by:

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

$p_{D.ext}$ 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.

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:

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

Examples

data(caribbean_3_model)
params <- setDetritusParams(caribbean_3_model, external = 10)