Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning

• Published in: PloS one 2017-12, Vol.12 (12), p.e0188955-e0188955
• Main Authors: Dedman, Simon, Officer, Rick, Clarke, Maurice, Reid, David G, Brophy, Deirdre
• Format: Article
• Language: English
• Subjects: Applications software; Biology and Life Sciences; Computer and Information Sciences; Earth Sciences; Ecology and Environmental Sciences; Engineering and Technology; Marine resources conservation; People and Places; Planning; Science Policy; Technology application
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0188955

Marine resource managers and scientists often advocate spatial approaches to manage data-poor species. Existing spatial prediction and management techniques are either insufficiently robust, struggle with sparse input data, or make suboptimal use of multiple explanatory variables. Boosted Regression Trees feature excellent performance and are well suited to modelling the distribution of data-limited species, but are extremely complicated and time-consuming to learn and use, hindering access for a wide potential user base and therefore limiting uptake and usage. We have built a software suite in R which integrates pre-existing functions with new tailor-made functions to automate the processing and predictive mapping of species abundance data: by automating and greatly simplifying Boosted Regression Tree spatial modelling, the gbm.auto R package suite makes this powerful statistical modelling technique more accessible to potential users in the ecological and modelling communities. The package and its documentation allow the user to generate maps of predicted abundance, visualise the representativeness of those abundance maps and to plot the relative influence of explanatory variables and their relationship to the response variables. Databases of the processed model objects and a report explaining all the steps taken within the model are also generated. The package includes a previously unavailable Decision Support Tool which combines estimated escapement biomass (the percentage of an exploited population which must be retained each year to conserve it) with the predicted abundance maps to generate maps showing the location and size of habitat that should be protected to conserve the target stocks (candidate MPAs), based on stakeholder priorities, such as the minimisation of fishing effort displacement. By bridging the gap between advanced statistical methods for species distribution modelling and conservation science, management and policy, these tools can allow improved spatial abundance predictions, and therefore better management, decision-making, and conservation. Although this package was built to support spatial management of a data-limited marine elasmobranch fishery, it should be equally applicable to spatial abundance modelling, area protection, and stakeholder engagement in various scenarios.