The zoon r package for reproducible and shareable species distribution modelling
Nick Goldinga b✉, Tom Augustc d, Tim C. D. Lucase f, David J. Gavaghang h, E. Emiel van Looni j, Greg McInernyk l
- aSchool of BioSciences University of Melbourne Parkville Vic. Australia
- bSchool of BioSciences, University of Melbourne, Parkville, Vic., Australia
- cNERC Centre for Ecology &
- dHydrology Crowmarsh Gifford, Wallingford UK
- eOxford Big Data Institute Li Ka Shing Centre for Health Information and Discovery Nuffield Department of Medicine University of Oxford Oxford UK
- fOxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery Nuffield Department of Medicine, University of Oxford, Oxford, UK
- gDepartment of Computer Science University of Oxford Oxford UK
- hDepartment of Computer Science, University of Oxford, Oxford, UK
- iInstitute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
- jInstitute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- k
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Abstract
Abstract The rapid growth of species distribution modelling (SDM) as an ecological discipline has resulted in a large and diverse set of methods and software for constructing and evaluating SDMs. The disjointed nature of the current SDM research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users. The zoon r package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows. zoon modules are interoperable snippets of r code, each carrying a SDM method that zoon combines into a single analysis object. Rather than defining these modules, zoon draws modules from an open, version‐controlled online repository. zoon makes it easy for SDM researchers to contribute modules to this repository, enabling others to rapidly deploy new methods in their own workflows or to compare alternative methods. Each workflow object created by zoon is a rerunnable record of the data, code and results of an entire SDM analysis. This can then be easily shared, scrutinised, reproduced and extended by the whole SDM research community. We explain how zoon works and demonstrate how it can be used to construct a completely reproducible SDM analyses, create and share a new module, and perform a methodological comparison study.
TL;DRThe zoon r package is explained and demonstrated how it can be used to construct a completely reproducible SDM analyses, create and share a new module, and perform a methodological comparison study. (Semantic Scholar)