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: Text
• Language: English
• Published: John Wiley & Sons, Inc. 2022
• Subjects: Statistical Reports; Gulf of Alaska; Pacific; Canis lupus; fratercula; Alaska
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9286827/; http://www.ncbi.nlm.nih.gov/pubmed/35060624; https://doi.org/10.1002/ecy.3637

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.