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RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and species’ responses to environmental change

View ORCID ProfileAnne-Kathleen Malchow, View ORCID ProfileGreta Bocedi, Stephen C. F. Palmer, View ORCID ProfileJustin M. J. Travis, View ORCID ProfileDamaris Zurell
doi: https://doi.org/10.1101/2020.11.17.384545
Anne-Kathleen Malchow
1University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
2Humboldt University of Berlin, Geography Department, Berlin, Germany
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  • For correspondence: malchow@uni-potsdam.de
Greta Bocedi
3School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ UK
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Stephen C. F. Palmer
3School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ UK
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Justin M. J. Travis
3School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ UK
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Damaris Zurell
1University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
2Humboldt University of Berlin, Geography Department, Berlin, Germany
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Abstract

  1. Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species’ distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses.

  2. We present RangeShiftR, an R package that provides flexible and fast simulations of spatial eco-evolutionary dynamics and species’ responses to environmental changes. It implements the individual-based simulation software RangeShifter for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package’s functionality, describe the underlying model structure with its main components and present a short example.

  3. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with comprehensive documentation and elaborate tutorials to provide a low entry level. Thanks to the implementation of the core code in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible.

  4. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification, and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 19, 2020.
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RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and species’ responses to environmental change
Anne-Kathleen Malchow, Greta Bocedi, Stephen C. F. Palmer, Justin M. J. Travis, Damaris Zurell
bioRxiv 2020.11.17.384545; doi: https://doi.org/10.1101/2020.11.17.384545
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RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and species’ responses to environmental change
Anne-Kathleen Malchow, Greta Bocedi, Stephen C. F. Palmer, Justin M. J. Travis, Damaris Zurell
bioRxiv 2020.11.17.384545; doi: https://doi.org/10.1101/2020.11.17.384545

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