Coral reefs of the Anthropocene are increasingly threatened by a range of human-induced stressors from anthropogenic local drivers of loss including overfishing, pollution, and coastal development, to regional stressors such as climate change and ocean acidification. The cumulative impacts of these stressors have significantly altered the structure, function, and composition of coral reef ecosystems worldwide. One of the most documented consequences is the sustained decline in hard coral cover exacerbated by mass bleaching events driven by anomalously high sea surface temperatures such as those recorded in 1998, 2010, and 2014-2017, and most recently during the Fourth Global Mass Bleaching Event. Beyond these ecological changes, coral reef degradation undermines the ability of these ecosystems to provide vital services to human populations including coastal protection, food security through fisheries, and income from tourism.
Established in 1995 as an operational network of the International Coral Reef Initiative (ICRI), the Global Coral Reef Monitoring Network (GCRMN) plays a central role in global coral reef monitoring efforts. Working through ten regional nodes - including the Pacific - the GCRMN produces regular syntheses of the status and trends of coral reefs based on harmonized scientific data. The network’s mission is to improve understanding of reef health, support evidence-based policy and management, and build the technical and human capacity for reef monitoring at local, national, and regional levels. The GCRMN’s global and regional reports are designed for policymakers, managers, researchers, and international organizations to guide conservation strategies and help countries meet their national and international biodiversity commitments. In combining science, capacity building, and policy relevance, the GCRMN is a cornerstone of efforts to safeguard coral reefs in an era of accelerating environmental change. Since its establishment, the GCRMN has published six global reports. Alongside these global assessments, the GCRMN has produced numerous regional and thematic reports focusing on the status and trends of coral reefs in specific regions, such as the Western Indian Ocean, the Pacific, and the East Asian Seas.
This GitHub repository accompanies the Status and Trends of Caribbean Coral Reefs: 1970-2024 GCRMN report, which provides a comprehensive overview of the status and trends of shallow-water coral reefs across the Caribbean region. The report addresses key questions about changes in benthic cover (hard coral, macroalgae, turf algae, coralline algae, and other fauna) and evolving threats to reef ecosystems over the last four decades. It includes analyses of major coral genera (Acropora, Orbicella, and Porites), as well as environmental stressors such as human population pressure, thermal stress (SST trends and anomalies), and cyclone activity. Structured in two main parts — a regional synthesis and 44 country and territory chapters — it combines biophysical monitoring data with local insights through 9 case studies. This GitHub repository provides the code used to produce the results of the report.
combine_model_data.RCombine benthic cover model results.combine_plot_trends.RCombine temporal trend plots produced by the function plot_trends.R.create_chapter_doc.qmdCountries and territories chapter template.data_descriptors.RGet number of sites, surveys, datasets, first and last year of monitoring.download_predictors.RDownload predictors extracted through GEE and stored on Google Drive.extract_coeff.RExtract linear models a and b coefficients.extract_mankendall.RCalculate temporal trends using Man Kendall test.graphical_par.RGraphical parameters, including colors and fonts.plot_pred_obs.RPlot predicted vs observed values (model evaluation).plot_region.RRegional background map.plot_residuals.RPlot residuals (model evaluation).plot_trends.RPlot temporal trends.plot_vimp.RPlot Variable Importance Plot (VIMP).prepare_benthic_data.RPrepare benthic cover data.plot_pdp.RPlot Partial Dependence Plot (PDP).plot_prediction_map.RPlot the map of the Caribbean with predicted values.render_qmd.RRender script create_chapter_doc.qmd.theme_graph.RMain ggplot theme for plots.theme_map.RMain ggplot theme for maps.theme_map_area.Rggplot theme for countries and territories maps.
a01_select_topo-bathy.jsExtract topography and bathymetry using Google Earth Engine (GEE).a02_clean_shp.RClean shapefiles from different sources.a03_select_benthic-data.RExtract benthic cover data from gcrmndb_benthos.a04_benthic-data_sources.RExtract lists of datasetID and contributors details.a05_reef-buffer.jsCreate coral reef buffer polygons at 20, 50, and 100 km using GEE.a06_reef-buffer-area.RJoin reef buffer with areas’ boundaries.a07_clean_cyclones.RClean cyclones data.a08_download_crw-year.RExtract netCDF file aggregated per year from Coral Reef Watch (CRW).
b01_extract_indicator_population.jsExtract population indicators using GEE.b02_extract_indicator_sst.RExtract SST indicators.b03_extract_indicator_cyclones.RExtract cyclones indicators.
c01_explo_benthic-data.qmdExploratory analyses of benthic cover data.c02_select_pred-sites.jsGenerate sites on which the predictions will be made.c03_extract_predictor_gee.jsExtract predictors on GEE.c04_extract_predictor_gravity.RExtract gravity as a predictor.c05_extract_predictor_enso.RExtract ENSO as a predictor.c06_extract_predictor_cyclones.RExtract cyclones as a predictor.c07_extract_predictor_crw.RExtract CRW derived predictors.c08_model_data-preparation.RCombine predictors and prepare benthic cover data.c09_xgboost-model.RRun XGBoost models.
d01_materials-and-methods.RProduce figures for the Materials and Methods.d02_region_map.RProduce map of the region.d03_areas_map.RProduce contextual maps for areas.d04_region_sst.RProduce figures for SST for the region.d05_areas_sst.RProduce figures for SST for areas.d06_region_cyclones.RProduce figures for cyclones for the region.d07_areas_cyclones.RProduce figures for cyclones for areas.d08_region_spatio-temporal.RProduce figures for spatio-temporal distribution of monitoring for the region.d09_areas_spatio-temporal.RProduce figures for spatio-temporal distribution of monitoring for areas.d10_benthic-cover_trends.RProduce figures for benthic cover temporal trends.d11_other-indicators.RProduce figures, tables, and numbers for other indicators.d12_fish-biomass.RProduce figure for the fish biomass box.d13_case-study.RProduce figures for the case studies.
e01_create-chapters.RGenerate .docx chapters for areas.e02_authors-contribution.RExport author’s contributions .xlsx file.e03_push-google-drive.RExport figures to the Google Drive folder.
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