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.

Modelled density of the seapen Kophobelemnon stelliferum in the North East Atlantic. The Random Forest density model trained on data collected by an ROV was constrained by an ensemble of Maxent and Random Forest presence-absence model trained on a larger dataset also collected by an ROV. This species provides structural complexity in an environment where it is lacking and, thus, promotes higher biodiversity where they settle. They are vulnerable to mechanical disturbance of the sediment by fishing gear and a better understanding of their distribution will lead to better management of their population. This work was performed at the University of Plymouth in 2021.

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.

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

Species distribution models (GAM, Maxent and Random Forest ensemble) predicting the distribution of discrete Lophelia pertusa - Desmophylum pertusum colonies assemblage in the Celtic Sea. This community is considered ecologically coherent according to the cluster analysis conducted by Parry et al. (2015) on image samples. 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.

Species distribution models (GAM, Maxent and Random Forest ensemble) predicting the distribution of Acanella arbuscula 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 (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 (GAM, Maxent, and Random Forest ensemble) predicting the distribution of Sea pens and burrowing megafauna assemblages in the Northeast Atlantic. This community is considered ecologically coherent according to the cluster analysis conducted by Parry et al. (2015) on image samples. Modeling 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.