Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie

• Published in: Ecology
• Main Authors: Thorson, James T., Arimitsu, Mayumi L., Levi, Taal, Roffler, Gretchen H.
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2022
• Subjects: Canis lupus; fratercula; Alaska
• Online Access: http://dx.doi.org/10.1002/ecy.3637; https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3637; https://onlinelibrary.wiley.com/doi/full-xml/10.1002/ecy.3637; https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3637

Abstract Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R ( mgcv and ggplot2 ) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins ( Fratercula cirrhata ) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves ( Canis lupus ligoni ) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines.