Data and code for: Mapping Fish Communities Across Environmental Gradients and Protection Boundaries Using HSMC

Data and code supporting the analyses presented in 'Mapping Fish Communities Across Environmental Gradients and Protection Boundaries Using Hierarchical Joint Species Distribution Modelling.' This repository contains R scripts for hierarchical Random Forest habitat classification, HMSC model fitting and spatial prediction, species clustering, and community mapping. Input data include BRUVS species count matrices (MaxN), habitat classification training data, environmental terrain derivative raster layers (5 m resolution, derived from multibeam sonar and airborne LiDAR), and the marine protected area boundary shapefile. A README file describes the workflow, script execution order, and data contents.