Set algae parameters for mizerReef

Usage

setAlgaeParams(
  params,
  algae_growth_initial = NULL,
  algae_capacity = NULL,
  UR_interaction = NULL,
  use_UR_cc = FALSE,
  algae_colour = "darkseagreen3"
)

Arguments

params: A MizerParams object.
algae_growth_initial: Numeric. The fixed, literature-informed growth rate of algae in grams/m^2/year, held constant (not retuned to match consumption – see the "Algae as an unstructured resource" section above). Default is 2e3, near the upper end of the range implied by converting Caribbean algal turf net production estimates of ~110-475 g dry weight/m^2/year (Carpenter, R.C. (1986). Partitioning herbivory and its effects on coral reef algal communities. Ecological Monographs, 56, 345-363; consistent with the meta-analysis in Tebbett, S.B. & Bellwood, D.R. (2021). Algal turf productivity on coral reefs: A meta-analysis. Marine Environmental Research, 168, 105311) to the wet-mass units used elsewhere in mizerReef, using an approximate 20% dry-matter content for turf algae.
algae_capacity: Numeric. Carrying capacity for algae biomass in 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 all unstructured resources. Default is FALSE. This flag is stored in the other_params slot.
algae_colour: Character. Colour to use for algae in plots. Default is "darkseagreen3".

Value

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

Details

All algae-related parameters (growth rate, capacity) are stored in the algae component of other_params (i.e. other_params(params)$algae), 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.

Algae as an unstructured resource

 mizerReef supports algae as a non-size-structured resource,
 consumed primarily by herbivorous fish. This function sets
 the initial growth rate, system carrying capacity, and
 interaction strengths for algae, allowing for flexible
 diet preferences.

 The interaction strength (\eqn{\theta_{i,algae}}) for each
 species \eqn{i} determines how strongly that group feeds on
 algae. This can be set via the `interaction_algae` 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 initial growth rate (`algae_growth_initial`) and carrying
 capacity (`algae_capacity`) control the baseline production
 and maximum standing stock of algae, respectively. Unlike
 detritus, algal production on a reef is real primary production
 and is not driven by grazer demand, so `algae_growth_initial` is
 treated as a fixed, literature-informed constant: it is *not*
 reset by [reefSteady()]. Instead [reefSteady()] (via [tuneUR()]/
 [tuneUR_cc()]) solves for the algae *biomass* that is at steady
 state for this fixed production rate and the model's current
 abundances, so that, all else equal, reducing grazing pressure
 increases the resulting algae biomass rather than reducing
 production to compensate.

 Carrying capacity can be toggled with `use_UR_cc`. When enabled,
 algae 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.

Algae consumption

This rate deliberately does not depend on feeding level or the satiation species parameter (contrast with detritus_consumption(), which does): in mizerReef, satiation-mediated consumption is exclusive to detritivory. Increases in herbivorous fish density following coral bleaching events suggest that reef herbivores respond to increased food availability without regulating their consumption (Ledlie et al. 2007; Pratchett et al. 2008; Khalil et al. 2013; Elma et al. 2023), and Caribbean herbivores have been observed to fill their gut up to three times a day (Ferreira et al. 1998; Kopp et al. 2010). Algal depletion is therefore modelled as driven by continuous grazing pressure rather than by any individual consumer's satiation state. getAlgaeConsumption() reports the feeding-level-adjusted rate actually ingested by each species for diagnostic purposes, but that adjusted rate is not what depletes the algae pool or what tuneUR()/tuneUR_cc() use for tuning.

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:

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

Examples

data(caribbean_3_model)
params <- setAlgaeParams(caribbean_3_model, algae_growth_initial = 2500)