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SSNdesign—An R package for pseudo-Bayesian optimal and adaptive sampling designs on stream networks

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  • Alan R Pearse
  • James M McGree
  • Nicholas A Som
  • Catherine Leigh
  • Paul Maxwell
  • Jay M Ver Hoef
  • Erin E Peterson

Abstract

Streams and rivers are biodiverse and provide valuable ecosystem services. Maintaining these ecosystems is an important task, so organisations often monitor the status and trends in stream condition and biodiversity using field sampling and, more recently, autonomous in-situ sensors. However, data collection is often costly, so effective and efficient survey designs are crucial to maximise information while minimising costs. Geostatistics and optimal and adaptive design theory can be used to optimise the placement of sampling sites in freshwater studies and aquatic monitoring programs. Geostatistical modelling and experimental design on stream networks pose statistical challenges due to the branching structure of the network, flow connectivity and directionality, and differences in flow volume. Geostatistical models for stream network data and their unique features already exist. Some basic theory for experimental design in stream environments has also previously been described. However, open source software that makes these design methods available for aquatic scientists does not yet exist. To address this need, we present SSNdesign, an R package for solving optimal and adaptive design problems on stream networks that integrates with existing open-source software. We demonstrate the mathematical foundations of our approach, and illustrate the functionality of SSNdesign using two case studies involving real data from Queensland, Australia. In both case studies we demonstrate that the optimal or adaptive designs outperform random and spatially balanced survey designs implemented in existing open-source software packages. The SSNdesign package has the potential to boost the efficiency of freshwater monitoring efforts and provide much-needed information for freshwater conservation and management.

Suggested Citation

  • Alan R Pearse & James M McGree & Nicholas A Som & Catherine Leigh & Paul Maxwell & Jay M Ver Hoef & Erin E Peterson, 2020. "SSNdesign—An R package for pseudo-Bayesian optimal and adaptive sampling designs on stream networks," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-17, September.
  • Handle: RePEc:plo:pone00:0238422
    DOI: 10.1371/journal.pone.0238422
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    References listed on IDEAS

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    1. C. J. Vörösmarty & P. B. McIntyre & M. O. Gessner & D. Dudgeon & A. Prusevich & P. Green & S. Glidden & S. E. Bunn & C. A. Sullivan & C. Reidy Liermann & P. M. Davies, 2010. "Global threats to human water security and river biodiversity," Nature, Nature, vol. 467(7315), pages 555-561, September.
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    1. Matthew Heiner & Matthew J. Heaton & Benjamin Abbott & Philip White & Camille Minaudo & Rémi Dupas, 2023. "Model-Based Clustering of Trends and Cycles of Nitrate Concentrations in Rivers Across France," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 28(1), pages 74-98, March.
    2. AWLP Thilan & P Menéndez & JM McGree, 2023. "Assessing the ability of adaptive designs to capture trends in hard coral cover," Environmetrics, John Wiley & Sons, Ltd., vol. 34(6), September.

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