SSNbayes: An R Package for Bayesian Spatio-Temporal Modelling on Stream Networks

School of Mathematical Sciences, Queensland University of Technology

santosfe@qut.edu.au

Marine Mammal Laboratory, NOAA-NMFS Alaska Fisheries Science Center.

jay.verhoef@noaa.gov

School of Mathematical Sciences, Queensland University of Technology

james.mcgree@qut.edu.au

Rocky Mountain Research Station, US Forest Service

Daniel.isaak@usda.gov

School of Mathematical Sciences, Queensland University of Technology

k.mengersen@qut.edu.au

EP Consulting

erin@peterson-consulting.com

Abstract

Spatio-temporal models are widely used in many research areas from ecology to epidemiology. However, a limited number of computational tools are available for modeling river network datasets in space and time. In this paper, we introduce the R package SSNbayes for fitting Bayesian spatio-temporal models and making predictions on branching stream networks. SSNbayes provides a linear regression framework with multiple options for incorporating spatial and temporal autocorrelation. Spatial dependence is captured using stream distance and flow connectivity while temporal autocorrelation is modelled using vector autoregression approaches. SSNbayes provides the functionality to make predictions across the whole network, compute exceedance probabilities, and other probabilistic estimates, such as the proportion of suitable habitat. We illustrate the functionality of the package using a stream temperature dataset collected in the Clearwater River Basin, USA.

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