Calculate Reef-level Hard Coral Cover — calculate_reef

Calculate Reef-level Hard Coral Cover (HCC)

Usage

calculate_reef_hcc(
  spatial_grid,
  spde,
  all_effects_hcc,
  data_reefs_df,
  data_reefs_sf,
  reefs_poly_sf,
  config_sp
)

Arguments

spatial_grid: An sfc POINT object representing the spatial grid.
spde: A list containing the SPDE mesh, SPDE object, Q matrix, and A matrix.
all_effects_hcc: A matrix containing the synthetic hard coral cover field.
data_reefs_df: A data.frame of reef sample points with columns Longitude and Latitude.
data_reefs_sf: An sf object of the reef sample points.
reefs_poly_sf: An sf polygon object of reef boundaries.
config_sp: A list containing config_spuration parameters, including years.

Value

A list containing:

data_reefs_sample_hcc – HCC values at the sample-level.
data_reefs_hcc – Reef-level HCC values in long format with Year and Value.
data_reefs_pts_hcc_sf – Reef-level HCC values as an sf object.

Details

Calculates reef-level hard coral cover (HCC) by projecting the spatially explicit synthetic hard coral cover field onto reef polygons. This function aggregates cover estimates from the spatial grid to reef-specific samples and returns the data in both tabular and sf formats.

Author

Murray