Reproducible statistical modelling framework

Content

This repository contains the results presented in the paper “Predicting coral trends and attributing drivers of change from local to global scales” by Vercelloni et al.

The files Appendix_A.html and Appendix_B.html correspond to the manuscript appendices. They can be reproduced following these simple instructions:

In the Appendix_A folder, the code is stored in the scripts/ directory. The scripts should be run in sequence. The final script, 8.report.qmd, automatically generates the visualizations in HTML format (e.g., quarto render 8.report.qmd). Note that the folder figures needs to be manually created.

In the Appendix_B folder, the appendix_B.qmd file contains the code to run the statistical modelling pipeline for the four scenarios described in the paper. Once the pipeline has finished running, this file can be rendered to automatically visualize the results (e.g., quarto render appendix_B.qmd).

Data tables

Monitoring and disturbance data are provided in the Appendix_A/data folder, which contains three files:

• reef_data_aggregated.csv: observations of coral cover at data-tier locations. The table contains eight variables - Tier5 (data-tier identifier), fYEAR (survey year), COUNT (count of coral cover), TOTAL (total point count), n_obs (number of monitored sites within the data-tier), COVER (percent coral cover), and geolocation coordinates of each data-tier.
• hexpred.shp: a shapefile containing disturbance information across all tiers. The table contains 18 variables with Tier5 (all-tier identifier), fYEAR (survey year), svrty_d* (severity of heat stress and associated time lags), max_dhw* (maximum values of degree heating weeks for the survey year and associated time lags), svrty_c* (severity of cyclone exposure and associated time lags), max_cyc* (maximum cyclone exposure for the survey year expressed as hours of exposure to cyclonic waves and associated time lags), As_Data (yes if Tier5 is a data-tier, no is Tier5 is a predictive-tier), reefid (reef(s) identifier within the Tier5), reef_ar (portion of the Tier5 that contains coral reefs in square metres), geometry (geolocation of the Tier5).
• MarineWaterBodiesV2_4: a shapefile indicating inshore and offshore reef zones along the Great Barrier Reef.

To cite the data, please use: Australian Institute of Marine Science (AIMS). (2025). ReefCloud public data (Australia, 2006–2024). Retrieved from https://apps.aims.gov.au/metadata/view/1997de64-b274-427f-8cdc-d01b54e623f9 (accessed 01-Dec-2025).

License

This repository is provided by the authors under the MIT License (MIT).

Bug reporting

• Please report any issues or bugs.