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 Plankton Lifeform Extraction Tool brings together disparate European plankton datasets into a central database from which it extracts abundance time series of plankton functional groups, called “lifeforms”, according to shared biological traits. This tool has been designed to make complex plankton datasets accessible and meaningful for policy, public interest, and scientific discovery. The Plankton Lifeform Extraction Tool currently integrates 155 000 samples, containing over 44 million plankton records, from nine different plankton datasets within UK and European seas, collected between 1924 and 2017. Additional datasets can be added, and time series can be updated.

Species distribution models (Random Forest) predicting the distribution of mixed cold-water coral community (Coral Garden) assemblage in the Celtic Sea. This community is considered ecologically coherent according to the cluster analysis conducted by Parry et al. (2015) on image sample. Modelling its distribution complements existing work on their definition and offers a representation of the extent of the areas of the North East Atlantic where they can occur based on the best available knowledge. This work was performed at the University of Plymouth in 2021.

Script for performing the Mission Atlantic RISK Analysis. It has been modified from the ODEMM ('Options for Delivering Ecosystem-Based Marine Management') - approach. For details see https://doi.org/10.3389/fmars.2022.1037878

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.

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

An R Package that provides supporting functions for conducting Integrated Ecosystem Assessments (IEA), developed in the framework of Mission Atlantic. The package includes methods for data exploration and assessment of the current ecosystem status. Forked repository in Mission Atlantic. For latest version, check the original repository.

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.

Species distribution models (GAM, Maxent and Random Forest ensemble) predicting the distribution of Solenosmilia variabilis reef assemblage in the Celtic Sea. This community is considered ecologically coherent according to the cluster analysis conducted by Parry et al. (2015) on image sample. Modelling its distribution complements existing work on their definition and offers a representation of the extent of the areas of the North East Atlantic where they can occur based on the best available knowledge. This work was performed at the University of Plymouth in 2021.

Species distribution models (Maxent) predicting the distribution of two Vulnerable Marine Ecosystems (VME): the reef-forming Scleractinian coral Desmophyllum pertusum and the aggregations forming Hexactinellid sponge Pheronema carpenteri. Both of these species are VME indicator taxa and form habitat that enhance deep-sea diversity (Ross and Howell, 2013). Maps of the likely distribution of the habitat formed by these two species will enable efficient Marine Spatial planning to facilitate their conservation. This work was performed at the University of Plymouth in 2021. A GIS layer is provided for each species.