Generate Settings for Synthetic Reef Simulations

Generate Simulation Settings for Synthetic Reef Landscapes

Usage

generateSettings(nreefs, nsites, nyears, dhw_eff, cyc_eff, other_eff)

Arguments

nreefs

Integer. Number of reef locations to simulate.

nsites

Integer. Number of sites to simulate per reef.

nyears

Integer. Number of years to simulate.

dhw_eff

Numeric. Weight controlling the influence of thermal stress (degree heating weeks) on benthic cover.

cyc_eff

Numeric. Weight controlling the influence of cyclone disturbances on benthic cover.

other_eff

Numeric. Weight for additional disturbances not explicitly modelled.

Value

Invisibly returns a list containing the four configuration lists: config_sp, config_lrge, config_fine, and config_pt. Each is also assigned to the global environment.

Details

Creates and stores all configuration lists required to simulate synthetic reef landscapes, including spatio-temporal settings, large-scale sampling structure, fine-scale sampling hierarchy, and point-based observation parameters. Each configuration list is also exported to the global environment for downstream modelling functions.

Spatio-temporal parameters (config_sp)

Controls the spatial domain, covariance structure, temporal sequence, and disturbance weights.

• seed: Random seed controlling all stochastic processes.

• crs: Coordinate reference system (EPSG code).

• model: Variogram model (e.g., "Exp", "Sph", "Gau", "Mat", etc.).

• psill: Partial sill (variance explained by spatial structure).

• range: Distance at which spatial correlation becomes negligible.

• nugget: Variance at zero distance (micro-scale variability).

• alpha: Smoothness of the spatial field.

• kappa: Spatial scale parameter in the SPDE representation.

• variance: Variance of the Matérn precision matrix.

• patch_threshold: Threshold defining habitat patches.

• reef_width: Half-width of the simulated reef ribbon.

• years: Sequence of simulated years.

• dhw_weight: Weight of thermal stress (degree heating weeks).

• cyc_weight: Weight of cyclone disturbances.

• other_weight: Weight of additional disturbance processes.

• hcc_cover_range: Expected range of hard coral cover.

• hcc_growth: Annual growth rate of hard coral cover.

• sc_cover_range: Expected range of soft coral cover.

• sc_growth: Annual growth rate of soft coral cover.

Large-scale sampling parameters (config_lrge)

• n_locs: Number of reef locations.

• n_sites: Number of sites per reef.

• seed: Seed for sampling reproducibility.

Fine-scale sampling parameters (config_fine)

Defines site-level, transect-level, and residual variance components for each benthic group.

• years: Years included in the fine-scale simulation.

• Number_of_transects_per_site: Transects simulated at each site.

• Depths: Number of depth strata.

• hcc_site_sigma, hcc_transect_sigma, hcc_sigma: Random-effect variances for hard coral.

• sc_site_sigma, sc_transect_sigma, sc_sigma: Random-effect variances for soft coral.

• ma_site_sigma, ma_transect_sigma, ma_sigma: Random-effect variances for macroalgae.

Point-based sampling parameters (config_pt)

Defines the structure of quadrats, frames, and annotation points.

• Depths: Number of depth strata.

• Depth_effect_multiplier: Strength of depth-related differences.

• Number_of_transects_per_site: Transects per site.

• Number_of_frames_per_transect: Frames per transect.

• Number_of_quadrats_per_transect: Quadrats per transect.

• Points_per_frame: Annotation points per frame.

• Quad_sigma: Quadrats-level random variation.

Author

Murray