mizerParams object for a simple, generic Caribbean reef with 3 species groups
Source:R/data.R
caribbean_3_model.RdA MizerParams object for a simple
Caribbean reef ecosystem model with three functional groups: predators,
herbivores, and invertebrates. It is built using the caribbean_3_species
and caribbean_3_interaction data, and includes all parameter settings and
calibrations as described in the associated PhD thesis and FORCE dataset.
This object can be used directly with mizer functions for simulation and
analysis.
Details
Recalibrated in 2026 against a corrected senescence-mortality formula
(reefSenMort()) – fish abundances, growth/consumption rates and
reproduction parameters were all re-tuned to restore a genuine steady
state under the corrected code (verified: repeated reefSteady() calls
leave biomass unchanged). Two herbivore species_params were also changed
from their original thesis values as part of this: satiation is now
TRUE (was FALSE) since herbivore biomass has no density-dependent
brake without some cap on individual intake once mortality is realistically
low – the realised feeding level is consistently close to 1, still
consistent with the citations behind the package's usual herbivore
default (Caribbean herbivores' guts observed to be full nearly
continuously); and age_mat is now 1.6 (was 4), the age at median
sexual maturity for Sparisoma viride (Rivera Hernandez & Shervette
2025), replacing a value that appears to have conflated it with that
species' age at sexual transition. See
inst/scripts/Caribbean_3_model-calibration.R's design note and
vignettes/caribbean_3_model-description.Rmd for the full reasoning.
Biomasses (predators/herbivores/inverts, g/m^2) are now 107.9/34.1/40.1,
matching the FORCE-survey targets (107/34/40) essentially exactly.
For details on parameter derivation, model calibration, and implementation, see Chapter 3 of the PhD Thesis: Beese, C. (2025). "Modelling Coral Reef Futures: Exploring the role of structural complexity in sustaining ecosystem services." Victoria University of Wellington.
References
FORCE dataset. From: Dryden, C. (2017). Habitat structural complexity of Caribbean coral reefs and its relationships with fish community structure. PhD Thesis, Newcastle University.
Beese, C. (2025). PhD Thesis. "Modelling Coral Reef Futures: Exploring the role of structural complexity in sustaining ecosystem services." Victoria University of Wellington. https://doi.org/10.26686/wgtn.26421523