Upper limits of coral communities

This repository containds 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)

  Data files

  • coral_cover.csv: contains coral cover (Scleractinian corals) estimates from the manta tow surveys. Each row corresponds to one tow.

    • YEAR_CODE: financial year when the survey was conducted (e.g., 201415 is for 2014-2015)
    • REEF_NAME: reef
    • ZONE: wave exposure zone (flank1 and flank2 have intermediate wave exposure, front has high wave exposure, and back is sheltered)
    • HC_MIN: lower end of the hard coral cover interval
    • HC_MAX: upper end of the hard coral cover interval
    • Central_LAT: latitude at the center of the tow
    • Central_LON: longitude at the center of the tow
    • HARD_COVER: midpoint of the coral cover interval

  • environmental_variables.csv: contains the environmental variables for each site (wave exposure zone within reef)

    • Reef: reef
    • Zone: wave exposure zone (flank1 and flank2 have intermediate wave exposure, front has high wave exposure, and back is sheltered)
    • Latitude: site latitude
    • Longitude: site longitude
    • median_ubed90: 90^th quantile of horizontal water velocity at bed (m s^-1) (summarised as the median value for each site)
    • per_suitable: proportion of hards substrate available
    • Secchi_median: median Secchi depth (m)
    • temp_median: median temperature (degrees C)

    Output files

  • rds files: contain the fitted models, can be called in brms (using the file function) to avoid rerunning the models.

  • manuscript figures

    Code

    • analyses.R:
      • estimates upper limits from time series coral cover data
      • fits models
      • generates figures shown in the manuscript
    • functions.R:
      • includes the required functions to run the analyses