Status and Trends of Coral Reefs of the Pacific: 1980-2023

1. Introduction

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 areas, such as the Caribbean, the Western Indian Ocean, the Pacific, and the East Asian Seas.

This GitHub repository accompanies the Status and Trends of Coral Reefs of the Pacific: 1980-2023 GCRMN report, which provides a comprehensive overview of the condition and evolution of shallow-water coral reefs across the Pacific region. The report addresses key questions about changes in benthic cover (hard coral, macroalgae, turf algae, and coralline algae) and evolving threats to reef ecosystems over the last four decades. It includes analyses of major coral families (Acroporidae, Pocilloporidae, Poritidae), 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 individual country and territory chapters — it combines biophysical monitoring data with local insights, including case studies and socioeconomic perspectives where available. This GitHub repository provides the code used to produce the results of the report.

2. Code

Functions

combine_model_data.R Combine benthic cover model results.
combine_plot_trends.R Combine temporal trend plots produced by the function plot_trends.R.
create_chapter_doc.qmd Countries and territories chapter template.
data_descriptors.R Get number of sites, surveys, datasets, first and last year of monitoring.
download_predictors.R Download predictors extracted through GEE and stored on Google Drive.
extract_coeff.R Extract linear models a and b coefficients.
extract_mannkendall.R Calculate temporal trends using Man Kendall test.
graphical_par.R Graphical parameters, including colors and fonts.
plot_pdp.R Plot Partial Dependence Plot (PDP).
plot_pred_obs.R Plot predicted vs observed values (model evaluation).
plot_prediction_map.R Plot the map of the Caribbean with predicted values.
plot_raw_data.R Plot raw benthic data.
plot_residuals.R Plot residuals (model evaluation).
plot_trends.R Plot temporal trends.
plot_vimp.R Plot Variable Importance Plot (VIMP).
prepare_benthic_data.R Prepare benthic cover data.
render_qmd.R Render script create_chapter_doc.qmd.
theme_graph.R Main ggplot theme for the plots of the reports.
theme_map.R Main ggplot theme for the maps of the reports.

Cleaning and selection (`a_`)

a01_select_benthic-data.R Select gcrmndb_benthos data to use in the analyses.
a02_benthic_data_sources.R Extract data sources from gcrmndb_benthos.
a03_clean_eez.R Select and clean economic exclusive zones (EEZ) from marineregions.
a04_clean_land.R Clean Pacific land data (high spatial resolution) from Princeton University.
a05_clean_bathy.R Clean bathymetry data from Natural Earth Data.
a06_clean-reef-distribution.R Select Pacific coral reefs distribution from the Tropical Coral Reefs of the World World Resources Institute (WRI).
a07_reef-buffer.js Create 100 km reef buffer using Google Earth Engine (GEE).
a08_clean_cyclones.R Clean cyclone dataset from IBTrACS.
a09_download_crw-year.R Extract netCDF file aggregated per year from Coral Reef Watch (CRW) data.

Extract indicators (except benthic cover) (`b_`)

b01_extract_indicator_land.js Extract total land area for each EEZ using GEE.
b02_extract_indicator_elevation.js Extract mean land elevation for each EEZ using GEE.
b03_extract_indicator_population.js Extract human population for each EEZ using GEE.
b04_extract_indicator_sst.R Extract SST on coral reefs for each EEZ.
b05_extract_indicator_cyclones.R Extract cyclones on coral reefs for each EEZ.

Models (benthic cover) (`c_`)

c01_explo_benthic-data_files Exploratory analyses of benthic cover data.
c02_select_pred-sites.js Generate sites on which the predictions will be made.
c03_extract_predictor_gee.js Extract the values of the predictors for data sources available on GEE.
c04_extract_predictor_gravity.R Extract gravity as a predictor.
c05_extract_predictor_enso.R Extract ENSO as a predictor.
c06_extract_predictor_cyclones.R Extract cyclones as a predictor.
c07_extract_predictor_crw.R Extract CRW derived predictors.
c08_model_data-preparation.R Combine predictors and prepare observed data.
c09_model_tuning_xgb.R Machine Learning model hyperparameters tuning.
c10_model_bootstrap_xgb.R Machine Learning model bootstrap.

Figures and tables (`d_`)

d01_materials-and-methods.R Produce figures for the Materials and Methods.
d02_pacific_map.R Produce map of the region.
d03_territories_map.R Produce contextual maps for countries and territories.
d04_pacific_sst.R Produce figures for SST for the region.
d05_territories_sst.R Produce figures for SST for countries and territories.
d06_pacific_cyclones.R Produce figures for cyclones for the region.
d07_territories_cyclones.R Produce figures for cyclones for countries and territories.
d08_pacific_spatio-temporal.R Produce figures for spatio-temporal distribution of monitoring for the region.
d09_territories_spatio-temporal.R Produce figures for spatio-temporal distribution of monitoring for countries and territories.
d10_benthic-cover_trends.R Produce figures for benthic cover temporal trends.
d11_other-indicators.R Produce figures, tables, and numbers for other indicators.
d12_case-studies.R Produce figures for case studies.

Writing and sharing (`e_`)

e01_create-chapters.R Generate .docx chapters for countries and territories.
e02_authors-contribution.R Export authors’ contributions .xlsx file.

3. Reproducibility parameters

Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", :
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 pandoc   3.4 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
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 [1] C:/Users/jwicquart/AppData/Local/Programs/R/R-4.5.0/library

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Name		Name	Last commit message	Last commit date
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code		code
misc		misc
.gitignore		.gitignore
README.Rmd		README.Rmd
README.md		README.md
pacific_2023.Rproj		pacific_2023.Rproj

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Status and Trends of Coral Reefs of the Pacific: 1980-2023

1. Introduction

2. Code

Functions

Cleaning and selection (`a_`)

Extract indicators (except benthic cover) (`b_`)

Models (benthic cover) (`c_`)

Figures and tables (`d_`)

Writing and sharing (`e_`)

3. Reproducibility parameters

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Status and Trends of Coral Reefs of the Pacific: 1980-2023

1. Introduction

2. Code

Functions

Cleaning and selection (a_)

Extract indicators (except benthic cover) (b_)

Models (benthic cover) (c_)

Figures and tables (d_)

Writing and sharing (e_)

3. Reproducibility parameters

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Cleaning and selection (`a_`)

Extract indicators (except benthic cover) (`b_`)

Models (benthic cover) (`c_`)

Figures and tables (`d_`)

Writing and sharing (`e_`)

Packages