Code and data: Spatial variation in upper limits of coral cover on the Great Barrier Reef

Identifying the maximum coral cover that a coral community can sustain (i.e., its ‘upper limit’) is important for predicting community dynamics and improving management strategies. Here, we quantify the relationship between estimated upper limits and key environmental factors on coral reefs: hard substrate availability, temperature, and water clarity. We used 32 years (1990-2022) of data on coral cover around reef perimeters in the Great Barrier Reef, Australia. Each reef was divided into four wave exposure habitats depending on prevailing wind conditions. For each site, we determined if hard coral cover had reached a plateau or upper limit. Next, we extracted existing estimates of hard substrate availability, modelled water temperature, and Secchi depth. Then, we quantified the relationship between these environmental variables and the upper limits. We found varying upper limits across the GBR, with a median of 33% coral cover and only 17% of the estimated upper limits exceeded 50% cor..., Coral cover data
We used hard coral cover data from manta tow surveys conducted by the Australian Institute of Marine Science’s (AIMS) Long-term Monitoring Program (LTMP) from 1990 to 2022 (Emslie et al., 2020). Manta tow surveys quantified broadscale patterns in percent coral cover on a ten-meter swath of the reef slope around the entire perimeters of 173 reefs on the Great Barrier Reef, Australia (from 12°S to 24°S and 143°E to 152°E). Reefs were visited a maximum of once a year.
Each reef was divided into four reef zones or sites based on prevailing wind exposure: one back (leeward) site that was the most protected, one front (windward) site being the most exposed, and two flank sites with intermediate exposure. Sites were classified based on reef geomorphology and local knowledge of prevailing wind conditions. Each tow was assigned a reef zone, and from 2014 onwards, the tow paths were georeferenced. Depending on weather conditions and variable reef structure, following the exact pa..., , # Code and data: Spatial variation in upper limits of coral cover on the Great Barrier Reef

[https://doi.org/10.5061/dryad.ngf1vhj44](https://doi.org/10.5061/dryad.ngf1vhj44)

## Description of the data and file structure

### Upper limits of coral communities

This repository contains the data and code to reproduce the results of the manuscript \"Spatial variation in upper limits of coral cover on the Great Barrier Reef\".

The scripts were run in R version 4.3.2 using the following packages:

* brms (version 2.20.4)
* patchwork (version 1.2.0)
* viridis (version 0.6.4)
* dplyr (version 1.1.4)
* ggplot2 (version 3.5.1)

To run the code, the working directory must have three folders: *Data* (which should include *coral_cover.csv* and *environmental_variables.csv*), *Code* (which should contain *analyses.R* and *functions.R*), and *Outputs* (where models and plots will be saved).

### Files and variables

#### Data files

**coral_cover.csv**: contains coral cover (Scleractinian corals) es...