The code and files contained in this repository support replication of a broad-scale benthic habitat classification of the South Atlantic produced by McQuaid et al. (2023). We used statistical clustering algorithms to classify broad-scale (10km2) environmental data into distinct habitat classes, which reflect variation in physical conditions and we assume support distinct biological communities. We request that any use of the input data is referenced as per the table below, and that classification outputs are referenced as: McQuaid K. A. Bridges A. E. H., Howell K. L., Gandra T. B. R., de Souza V., Currie J. C., Hogg O. T., Pearman T. R. R., Bell J. B. B., Atkinson L. J., Baum D., Bonetti J., Carranza A., Defeo O., Furey T., Gasalla M. A., Golding N, Hampton S. L., Horta S., Jones D. O. B., Lombard A. T., Manca E., Marin Y., Martin S., Mortensen P., Passdore C., Piechaud N., Sink K. J. & Yool A. 2023. Broad-scale benthic habitat classification of the South Atlantic. Progress in Oceanography. DOI: https://doi.org/10.1016/j.pocean.2023.103016

The availability of user-friendly, high-resolution global environmental datasets is crucial for bioclimatic modelling. For terrestrial environments, WorldClim has served this purpose since 2005, but equivalent marine data only became available in 2012, with pioneer initiatives like Bio-ORACLE providing data layers for several ecologically relevant variables. Currently, the available marine data packages have not yet been updated to the most recent Intergovernmental Panel on Climate Change (IPCC) predictions nor to present times, and are mostly restricted to the top surface layer of the oceans, precluding the modelling of a large fraction of the benthic diversity that inhabits deeper habitats. To address this gap, we present a significant update of Bio-ORACLE for new future climate scenarios, present-day conditions and benthic layers (near sea bottom). The reliability of data layers was assessed using a cross-validation framework against in situ quality-controlled data. This test showed a generally good agreement between our data layers and the global climatic patterns. We also provide a package of functions in the R software environment (sdmpredictors) to facilitate listing, extraction and management of data layers and allow easy integration with the available pipelines for bioclimatic modelling.

NASA's OceanColor Web is supported by the Ocean Biology Processing Group (OBPG) at NASA's Goddard Space Flight Center. Our responsibilities include the collection, processing, calibration, validation, archive and distribution of ocean-related products from a large number of operational, satellite-based remote-sensing missions providing ocean color, sea surface temperature and sea surface salinity data to the international research community since 1996. As a Distributed Active Archive Center (DAAC), known as the Ocean Biology DAAC (OB.DAAC), we are responsible for the archive and distribution of satellite ocean biology data produced or collected under NASA EOSDIS, including those from historical missions and partner space organizations.

HydroWASTE is a spatially explicit global database of 58,502 wastewater treatment plants (WWTPs) and their characteristics. This database was developed by combining national and regional datasets with auxiliary information to derive or complete missing characteristics, including the amount of people served, the flow rate of effluents, and the level of treatment of processed wastewater. The HydroSHEDS river network with streamflow estimates was used to geo-reference plant outfall locations and to assess the distribution of wastewaters at a global scale. All wastewater treatment plants are co-registered to the global river network of the HydroRIVERS database via their estimated outfall locations.

MISSION ATLANTIC assesses the whole Atlantic, and ecosystem components at risk from natural hazards and the consequences of human activities, including individual regional Case Studies, and their interconnectivity. To do this, Mission Atlantic develops IEAs for seven regional Case Studies, in sub-Arctic and Tropical regions of the Atlantic Ocean, ranging from shelf seas to the mid-Atlantic Ridge: 1) Norwegian Sea 2) Celtic Sea 3) Canary Current 4) North Mid Atlantic Ridge 5) South Mid Atlantic Ridge 6) Benguela Current 7) South Brazilian Shelf

Understanding how much inorganic fertilizer (referred to as fertilizer) is applied to different crops at national, regional and global levels is an essential component of fertilizer consumption analysis and demand projection. Good information on fertilizer use by crop (FUBC) is rarely available because it is difficult to collect and time-consuming to process and validate. To fill this gap, a first global FUBC report was published in 1992 for the 1990/1991 period, based on an expert survey conducted jointly by the Food and Agriculture Organization (FAO) of the UN, the International Fertilizer Development Center (IFDC) and the International Fertilizer Association (IFA). Since then, similar expert surveys have been carried out and published every two to four years in the main fertilizer-consuming countries. Since 2008 IFA has led these efforts and, to our knowledge, remains the only globally available data set on FUBC. This dataset includes data (in CSV format) from a survey carried out by IFA to represent the 2017–18 period as well as a collation of all historic FUBC data.

Water column sonar data, the acoustic back-scatter from the near-surface to the seafloor, are used to assess physical and biological characteristics of the ocean including the spatial distribution of plankton, fish, methane seeps, and underwater oil plumes. In collaboration with NOAA's National Marine Fisheries Service (NMFS) and the University of Colorado Boulder, NOAA’s National Centers for Environmental Information (NCEI) established a national archive for water column sonar data. This project entails ensuring the long-term stewardship of well-documented water column sonar data, and enabling discovery and access to researchers and the public around the world. Data providers include NOAA National Marine Fisheries Service (NMFS), NOAA Office of Ocean Exploration and Research (OER), NOAA National Ocean Service (NOS), Rolling Deck to Repository (R2R), U.S. academic and private institutions, and international groups. This data set comprises the water-column sonar data archived at NCEI in a more readily accessible media. Data provided to NCEI are in their raw format. Processing routines are being applied to a subset of the archive, specifically focusing on Simrad EK60 single and multiple frequency datasets. Ping alignment, noise removal algorithms (De Robertis & Higgenbottom, 2007; Ryan et al., 2015), and bottom detection algorithms are applied to the raw data binned into one hour intervals using Echoview (Myriax, v.10). The processed data are exported as a CSV for each interval and each frequency.

The ecorisk package will be published under this repository soon. The ecorisk R package is designed to perform and analyse (ecosystem) risk assessments.

A marine end-to-end ecosystem model and R package. The aim is to represent the entire interconnected marine ecosystem (from physics and chemistry, to whales and fisheries in continental shelf regions) by exploring 'what if' experiments and explore uncertainty. View the application, the website or the latest publication.

Finding suitable ecological state indicators is challenging and cumbersome in stochastic and complex ecological systems. INDperform is an R package for validating the performance of ecological state indicators and assessing the ecological status based on a suite of indicators. The performance evaluation addresses the sensitivity and robustness of indicators.