Abstract
The ongoing evolution of tracer mixing models has resulted in a confusing array of software tools that differ in terms of data inputs, model assumptions, and associated analytic products. Here we introduce MixSIAR, an inclusive, rich, and flexible Bayesian tracer (e.g., stable isotope) mixing model framework implemented as an open-source R package. Using MixSIAR as a foundation, we provide guidance for the implementation of mixing model analyses. We begin by outlining the practical differences between mixture data error structure formulations and relate these error structures to common mixing model study designs in ecology. Because Bayesian mixing models afford the option to specify informative priors on source proportion contributions, we outline methods for establishing prior distributions and discuss the influence of prior specification on model outputs. We also discuss the options available for source data inputs (raw data versus summary statistics) and provide guidance for combining sources. We then describe a key advantage of MixSIAR over previous mixing model software—the ability to include fixed and random effects as covariates explaining variability in mixture proportions and calculate relative support for multiple models via information criteria. We present a case study of Alligator mississippiensis diet partitioning to demonstrate the power of this approach. Finally, we conclude with a discussion of limitations to mixing model applications. Through MixSIAR, we have consolidated the disparate array of mixing model tools into a single platform, diversified the set of available parameterizations, and provided developers a platform upon which to continue improving mixing model analyses in the future.
Highlights
Mixing models, or models used to estimate the contribution of different sources to a mixture, are widely used in the natural sciences
How to cite this article Stock et al (2018), Analyzing mixing systems using a new generation of Bayesian tracer mixing models
The majority of mixing model applications use stable isotope values as tracers in efforts to assess the contribution of prey to a consumer diet, other applications include animal movement, pollutant sourcing, crossecosystem nutrient transfer, and sediment erosion fingerprinting (Bicknell et al, 2014; Bartov et al, 2012; Granek, Compton & Phillips, 2009; Blake et al, 2012)
Summary
Models used to estimate the contribution of different sources to a mixture, are widely used in the natural sciences. Versions of Bayesian mixing models treated the estimates of source-specific tracer means and variance as fixed (user specified), and only used raw mixture data in calculating the likelihood of source proportions (Moore & Semmens, 2008; Parnell et al, 2010). Case study: Alligator mississippiensis diet partitioning This case study highlights the main advantage of MixSIAR over previous mixing model software—the ability to include fixed and random effects as covariates explaining variability in mixture proportions and calculate relative support for multiple models via information criteria. Since the “Length + Individual” model estimates individuals’ diet proportions, we can plot the distribution of eind and see directly that most alligators are specialists (e > 0.8, Fig. 8). Nifong, Layman & Silliman (2015) performed a well-designed study, and their main conclusions are robust—we only reanalyze their data here to highlight advantages of MixSIAR over other mixing model software
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