ereefs

Overview

What is eReefs?

eReefs is a project that combines government commitment to reef protection, world-class science innovation and contributions from leading Australian businesses. It is a collaborative information system created (the Great Barrier Reef Foundation, CSIRO, the Australian Institute of Marine Science, Bureau of Meteorology, and Queensland Government) that provides a picture of what is currently happening on the reef, and what will likely happen in the future.

Focused on the protection and preservation of the iconic Great Barrier Reef, it forms the first step in building comprehensive coastal information systems for Australia. Using the latest technologies to collate data, and new and integrated modelling, eReefs will produce powerful visualisation, communication and reporting tools. It will provide for the Reef information akin to that provided by the Bureau of Meteorology for weather. This information will benefit government agencies, Reef managers, policy makers, researchers, industry and local communities.

What does the ereefs R package do?

The ereefs R package provides easy access to eReefs and other CSIRO-EMS output files. It can work with both the original curvilinear eReefs/EMS outputs hosted through the National Computational Infrastructure (NCI) eReefs data services and regularly regridded products that only provide cell centres, including the AIMS eReefs data service. Recent updates switch the package to a tidync/ncmeta-based access path so it remains usable against modern THREDDS/OPeNDAP servers. It can also be used to explore and visualise other CSIRO-EMS model output data, including output from RECOM model runs. CSIRO-EMS is the hydrodynamic-biogeochemical modelling software that underpins the eReefs models for the Great Barrier Reef. RECOM is an online interface that helps registered users to set up higher-resolution instances of CSIRO-EMS for small areas such as individual reefs that are nested within the eReefs models.

For depth-resolved variables, the package now treats layer = "surface" as the shallowest wet layer and layer = "bottom" as the deepest wet layer at each time-step. When eta is absent from a simple-format dataset, depth-below-free-surface helpers warn and assume eta = 0. When z_grid is absent but zc is available, the package reconstructs layer interfaces from zc using midpoint assumptions and resets the top interface to 1e20 to match the standard EMS convention. For scalar plotting workflows, viridis is now the default colour palette.

ereefs is designed to assist R users who need more customised access to eReefs data. This includes things like:

• Inspecting unfamiliar eReefs or EMS NetCDF files and THREDDS catalogs with inspect_ereefs_data() before extracting data. This provides a quick overview of spatial coverage, time coverage, available variables, units, dimension roles, and catalog files without reading full model arrays;

• Accessing data from versions of the eReefs model that are not available through the web-based data service;

• Accessing data for less commonly-used variables that are not included in the web-based data service or visualisation portal;

• Generating customised maps or animations for a specified region at a specified depth over a specified period of time, including (for example) true colour maps and animations from modelled optical data, maps that combine two or more eReefs variables (e.g., to get total zooplankton concentrations), maps with labelled points of interest such as Marine Monitoring Program (MMP) sampling locations, and maps with outlines of reef areas shown. Maps are created as ggplot2 figures and can be further adjusted as required by R users familiar with that package.

• Working across both grid styles now common in eReefs workflows:

  • curvilinear model grids where cell-corner coordinates are available and polygon geometry is needed for plotting;\
  • regular regridded products where only cell centres are supplied and the package reconstructs plotting geometry from the centre coordinates.

• Extracting and visualising data in different ways, for example:

  • Taking a vertical profile of a variable over the depth of the water column and displaying it either as a single profile at a point in time or as a depth-vs-time contour plot;\
  • Taking a two-dimensional vertical slice through the three-dimensional model data;\
  • Calculating vertically integrated results (i.e., the average value of a variable over the depth of the water column rather than the value at a particular depth);\
  • Extracting data along the path of a boat or glider.

How does this R package compare to the existing eReefs services?

Please see our online vignette to learn more about how this package compares to the multiple sources of eReefs exploration tools and platforms.

Installation

To install the latest release from GitHub use

if (!requireNamespace("remotes")) {
  install.packages("remotes")
}
remotes::install_github("open-aims/ereefs")

The current development version can be downloaded from GitHub via

if (!requireNamespace("remotes")) {
  install.packages("remotes")
}
remotes::install_github("open-aims/ereefs", ref = "dev")

Usage

Usage and further information about ereefs can be seen on the vignettes. Help files for the individual functions can be found on the reference page.

If you are upgrading from the older master workflow, please also read NEWS.md, which summarises the major behavioural and interface changes in the refactored development version.

Further Information

ereefs is provided by the Australian Institute of Marine Science under the MIT License (MIT).