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Fine-Scale Percent Cover

sampling_design_fine_scale_cover.Rd

Fine-Scale Percent Cover Estimates

Usage

sampling_design_fine_scale_cover(data_fixed_locs_obs, config_pt)

Arguments

data_fixed_locs_obs

An sf object representing fine-scale transect observations generated by sampling_design_fine_scale_fixed(). Must contain:

  • Reef, Site, Transect, Year, Date

  • HCC, SC, MA – benthic cover values

  • geometry associated with transects

config_pt_lrge

A list containing quadrat-level sampling parameters:

  • Depths – number of depths per transect

  • Depth_effect_multiplier – magnitude of depth effects

  • Number_of_quadrats_per_transect – number of quadrats

  • Quad_sigma – standard deviation of quadrat-level noise

  • seed – optional random seed

Value

An sf object containing quadrat-level percent cover values with:

  • Depth, Quadrats (Quad)

  • Group (HCC, SC, MA)

  • Percent cover values (Value) after depth + quadrat effects

  • all original transect identifiers and geometry

Details

Generates fine-scale percent cover estimates by expanding benthic cover values across quadrats. Applies depth effects, adds quadrat-level variation, and returns an sf object with quadrat-based percent cover suitable for downstream modelling and analysis.

This function:

  • expands transects across depth levels

  • reshapes benthic groups into long format

  • adds a depth effect using a scaled random component

  • generates quadrats and applies quadrat-level noise on the logit scale

  • converts back to percent cover (0–100%)

Author

Murray