DOI: 10.5061/dryad.wdbrv15vk
title: Derived variables and coordinates to assess the ecological relevance of multiscale bathymetry for coral species distribution modelling across the Great Barrier Reef

description: With constant improvements in the accuracy and availability of open-source
 digital elevation models (DEMs) comes a need to properly understand the
 relevance of their derived topographic variables in ecological research,
 particularly in marine environments. Here, we provide data and scripts
 used to investigate the ecological relevance of two open-source
 bathymetric models for deriving topographic variables to perform species
 distribution modelling of coral across the Great Barrier Reef (GBR),
 Australia. We illustrate our methods with a case study based on three
 common Acropora coral species (A. hyacinthus, A. spathulata, A.
 kenti) across 23 reefs of the GBR, where we produce high
 performing distribution maps using purely topographic variables derived
 from three open-access bathymetry models.  A script is provided
 to first download and process bathymetry DEMs from the Allen Coral Atlas
 and the DeepReef projects, before performing a multiscale generalisation
 to acquire these DEMs at  15m, 30m, 60m, 100m, 120m
 resolutions.  From these DEMs, we provide code for deriving 14
 topographic variables used in analyses. We provide the csv files
 containing values of the DEM and topographic variables at random
 assessment points across the 23 reefs,  as well as at the coral
 colony sample sites. The script contains all analyses, including DEM
 vertical depth assessment, variable correlations, and MaxEnt species
 distribution models.
description: Georeferenced <strong>coral occurrence data and depth
 measurements of three Acropora species </strong>were recorded within
 the context of coral adaptation research. Data was collected over three
 years (2021-2023) at 23 reefs spanning the extent of the Great Barrier
 Reef as part of the Reef Restoration and Adaptation Program (RRAP),
 targeting Acropora hyacinthus, Acropora spathulata and Acropora tenuis
 colonies. Here, coordinates, depth and health chart data of 2368 colonies
 are provided, alongside indications of which colony was used in specific
 analyses. Georeferenced coordinates were collected using a GPS towed
 behind divers during sampling campaigns, where timestamps on colony photos
 were used to find the associated coordinates. Colony depth was recorded
 using dive computers and corrected to the lowest astronomical tide using a
 custom R script. Details of the tide station along with the collection
 date’s tide levels are provided. The coordinates and corrected depths were
 used to investigate the accuracy of open-source bathymetric digital
 elevation models (DEMs) and to assess the ecological relevance of
 multiscale bathymetric topographic variables for regional species
 distribution modeling (SDM). Columns are provided to note the colonies
 used for DEM accuracy assessments, as well as those used in SDM
 analyses. <strong>Multiscale bathymetric digital
 elevation models (DEMs)</strong> and<strong> derived
 topographic variables</strong> used to characterise the seascape
 environment spanning the Great Barrier Reef Marine Park Authority (GBRMPA)
 region. This data was collected to investigate the accuracy of open-source
 bathymetric DEMs and to assess the ecological relevance of multiscale
 bathymetric topographic variables for regional species distribution
 modeling (SDM) of coral species. The base DEMs were downloaded from two
 publicly available online sources: the Allen Coral Atlas (ACA; Allen Coral
 Atlas, 2022; www.allencoralatlas.org) at approximately 10m resolution and
 the DeepReef Explorer (www.deepreef.org) at approximately 30m (Beaman,
 2017) and 100m (Beaman, 2010) resolutions. After processing, the base DEMs
 were generalised using a Gaussian pyramid algorithm: ACA from 15m to 30m,
 60m, 120m, DeepReef from 30m to 60m and 120m, as well as DeepReef at 100m.
 From each DEM, eight topographic variables were derived: slope (SLO),
 eastness (EAST), northness (NORTH), vertical curvature (VCU), horizontal
 curvature (HCU), vector ruggedness measure (VRM), sky view factor (SVF),
 bathymetric position index (BPI).  Variables are available as SAGA sdat
 files upon request. Variable values at all spatial resolutions from each
 bathymetry source are available as csv files: i) 15000 random points used
 to assess correlation and scatterplots, ii) 10000 random points used in
 MaxEnt SDM analyses, where points avoided areas that also contained
 presence data.
description: # Derived variables and coordinates to assess the ecological relevance of
 multiscale bathymetry for coral species distribution modelling across the
 Great Barrier Reef
 [https://doi.org/10.5061/dryad.wdbrv15vk](https://doi.org/10.5061/dryad.wdbrv15vk) This data accompanies the article '*Harnessing multiscale topographic environmental proxies in regional coral spatial modelling*' by Annie Guillaume, Renata Ferrari, Oliver Selmoni, Véronique Mocellin, Hugo Denis, Melissa Naugle, Emily Howells, Line Bay, and Stéphane Joost. Here, the accuracy of two open-source digital elevation models (DEMs) are assessed, along with the relevance of their derived topographic variables for use in marine ecological modelling. We provide scripts and relevant csv files to illustrate our methods with a case study based on three common *Acropora* coral species across the Great Barrier Reef, where we produce high performing distribution maps using purely topographic variables derived from three open-access bathymetry models. The environmental variables used in this study are described in the *Environmental_variable_Description.docx*. There we have provided the name of the variable, the abbreviation used in the datafiles and scripts, the description of the variable, the reference, and the parameters used to calculate the variable. More information on these variables are provided below. ## Description of the data and file structure The following files are used as inputs for the scripts, outlined at the end of the ReadMe **DEM raster files to produce variables (GBR_bathymetryDEM_multiscale.zip)** This is a very large zip file, containing rasters of the bathymetric DEMs  (as geotiffs - projected tiff files; .TIFF) from one of three DEM sources: Allen Coral Atlas (ACA15), DeepReef at 30m (gbr030), and DeepReef at 100m (gbr100). DEMs were generalised to different spatial resolutions: ACA from 15m to 30m, 60m and 120m. DeepReef 30m from 30m to 60m and 120m, and DeepReef 100 was kept at 100m. From these eight DEMS (3 sources at multiple resolutions), we extracted eight variables (described in *Environmental_variable_Description.docx*), such that we had 64 variables + 8 DEM values = 72 predictor variables in total. These GeoTiffs can be imported into R using the *terra* package, or into any GIS software (e.g., QGIS, SAGAGIS, GeoDa, ArchGIS, etc). Upon opening, the GeoTiff will appear as a raster format, which can be manipulated as required (e.g., change projection, crop to new size, etc). These were cropped using the shapefile (described below). Note that this folder does not need to be extracted for running the *MultiscaleMarineSDM_script.R* script, as the values that are used in the analyses have been extracted from the rasters (using the extract function of the Terra package in R) and are available in the csv files described below. **Shapefiles (GBRMPA_extent_max100m_WGS84.shp)** The shapefile '*GBRMPA_extent_max100m_WGS84.shp*' is provided to crop the DEMs to the study  region of the Great Barrier Reef. These files are provided for use in the *MultiscaleMarineSDM_producevariables_script.R ,* but can also be used if the User wishes to download their own variables from other repositories.  A shapefile is a file format for storing information about a vector alongside information about its projection on a map. Note that shapefiles require accessory files with the filenames ending in: *.cpg, . dbf, .prj, .shp, .shx*. Please download all the files together to ensure that they can be read by the software. The file ending in *.shp* is the one that needs to be provided if used in R or other GIS software (e.g., QGIS, SAGAGIS, GeoDa, ArchGIS, etc). Upon opening, the shapefile will appear as a vector format, which can be manipulated as required (e.g., change projection, crop to new size, etc). **CSV data files** In the following files, values are provided for the environmental variables, which have been extracted using the *MultiscaleMarineSDMscript**2*.R*. These values appear in the following CSV files with an abbreviated column name. The nomenclature follows the rule: "DEM source"**"resolution"*"*variable*": 1) the DEM source is either: Allen Coral Atlas (ACA15), DeepReef at 30m (gbr030), and DeepReef at 100m (gbr100); 2) the resolution is what the variable is generalised to: 015, 030, 060, 100, 120; and, 3) the variables, where the acronym corresponds to the variables listed in *Environmental_variableDescription.docx*.  **1.** **File**: *MultiscaleMarineSDM_presence_2368coral.csv* ***Coral coordinates:*** Coordinates collected within the framework of the RRAP (Reef Restoration and Adaptation Program) Column descriptions: * ID - Unique identifier for each colony * species - Species name (n=3; A. hyacinthus, A. spathulata, A. kenti) * ID.reef - Reef sampled (n=23) * X;Y - X,Y coordinates in UTM55 indexd on GDA2020 (epsg:7855) * decimalLatitude; decimalLongitude - Lat, Lon in WGS84 (epsg:4326) * collect.YEAR; collect.MONTH; collect.DAY; collect.TIME; collect.DATE - Date and time of collection * depth.raw.m; depth.correct.m.below: Tide_adjust - Depth as raw, LAT corrected, tide adjustment applied * DEMaccuracy - Boolean values to filter: 1 = used in DEM accuracy measurements ; 0 = not used in DEM accuracy measurements * SDManalysis - Boolean values to filter: 1 = used in SDM analyses ; 0 = not used in DSDM analyses * ACA15_015_DEM, gbr030... etc until the end - 72 predictor variable values, extracted from variable rasters using terra::extract(). These columns are named as described above **2.** **File**: *MultiscaleMarineSDM_variables_15000randompoints.csv* ***DEM and variable assessment points*** Coordinates of 15'0000 random background points, biased to coral sampled areas, only across 23 reefs Column description: * X;Y - X,Y coordinates in UTM55 indexd on GDA2020 (epsg:7855) * ACA15_015_DEM, gbr030... etc until the end - 72 predictor variable values, extracted from variable rasters using terra::extract(). These columns are named as described above **3.** **File**: *MultiscaleMarineSDM_variables_10000maxent.csv*  ***MaxEnt Background points*** Coordinates of 10'0000 random background points, biased to coral sampled areas, only across 23 reefs Column description: * X;Y - X,Y coordinates in UTM55 indexd on GDA2020 (epsg:7855) * ACA15_015_DEM, gbr030... etc until the end - 72 predictor variable values, extracted from variable rasters using terra::extract(). These columns are named as described above ## Sharing/Access information Some of the data are publicly available elsewhere. Links to other publicly accessible locations of the data, available from the Australian Institute for Marine Sciences (AIMS) server: * The **full RRAP coral colony metadata file**: used to obtain colony GPS and depth data; will be available online on the AIMS archive from November 2024.\ *Reference:* [https://doi.org/10.25845/8DJ4-0V58](https://doi.org/doi.org/10.5281/zenodo.3833242) * **Coordinates (X,Y, depth) records maintained by AIMS**\ *Reference:* Australian Institute of Marine Science (AIMS) (2024) Metadata associated with ethanol-preserved coral samples collected for the Reef Restoration and Adaptation Program’s Genetic Basis of Coral Traits project. Australian Institute of Marine Science (AIMS).\ [https://researchdata.edu.au/metadata-associated-ethanol-traits-project/2832117?fl](https://researchdata.edu.au/metadata-associated-ethanol-traits-project/2832117?fl) * **Multiscale DEMs and topographic variables**: Variables produced using the ***Produce_variables*** script (below) are available online on the AIMS archive.\ *Reference*: Australian Institute of Marine Science (AIMS). (2024) Multiscale bathymetric digital elevation models and derived topographic variables extending across the Great Barrier Reef. [https://doi.org/10.25845/ggyv-pq15](https://doi.org/10.25845/ggyv-pq15) Environmental data was derived from the following sources (also available from the zip folder provided: *GBR_multiscaleDEM.zip*): * **Allen Coral Atlas at allencoralatlas.org**\ *Reference:* Allen Coral Atlas (2022) Imagery, maps and monitoring of the world’s tropical coral reefs. [https://doi.org/10.5281/zenodo.3833242](https://doi.org/doi.org/10.5281/zenodo.3833242) Beaman, R.J. (2010) **DeepReef30m at** **pid.geoscience.gov.au/dataset/ga/115066**\ *Reference:* Beaman, R.J. (2017) High-resolution depth model for the Great Barrier Reef - 30 m dataset. *Geoscience Australia*. [https://doi.org/10.4225/25/5a207b36022d2](https://doi.org/10.4225/25/5a207b36022d2) * **DeepReef100m at deepreef.org/2010/07/06/gbr-bathy**\ *Reference:* Project 3D-GBR: A high-resolution depth model for the Great Barrier Reef and Coral Sea. Marine and Tropical Sciences Research Facility (MTSRF) Project 2.5i.1a Final Report. Cairns, Australia. [https://doi.org/10.4225/25/5a207b36022d2](https://doi.org/10.4225/25/5a207b36022d2) ## Code/Software We have provided the code necessary to replicate the results in the published article. These scripts require R (v4.1.0, 2021) to be installed, with the required packages are noted at the top of each script. If the user wishes to produce their own variables (***Produce_variables***), note that this also requires MatLab (MathWorks: MATLAB version R2019a) to be installed. As MatLab is a paid software, an alternative (but untested) R script is provided. Alternatively, the products of the script are provided, so that the ***Main script*** can be run. **Produce_variables**:\ An R script (*MultiscaleMarineSDM_producevariables_script.R*) outlining the **acquisition, processing and generalisation of open-source bathymetric DEMs** (available at the links above). These DEMs are cropped using the '*GBRMPA_extent_max100m_WGS84.shp*', which is a subset of the GBR marine protected area shapefile, to max depth of 100m. Note that it requires the use of MatLab for generalisation (code: *MultiscaleMarineSDM_producevariables_GaussianPyramid_MATLAB.mlx*), where alternative code in R is provided, but not tested. This script also outlines how to **derive topographic variables** used in downstream analyses. **Main script:**\ An R script (*MultiscaleMarineSDM_script*_2*.R*) to follow analyses of the article, including bathymetry DEM vertical assessment (comparing in-situ collected depth measurements with bathymetry estimated depths), derived variable correlations, and MaxEnt species distribution modelling analyses (parameter optimisation, full model, prediction rasters). Note that the final prediction raster across the GBR (section 7) will only run if the full 72 variables have been produced, as these files are not yet uploaded. ## Version Changes **13-apr-2025**: Script was updated to include author and publication metadata.