Abundance-mediated species interactions between coyote, fisher, and marten in Northeastern US

Ecological theory posits that the strength of interspecific interactions is fundamentally underpinned by the population sizes of the involved species. Nonetheless, contemporary approaches for modelling species interactions predominantly centre around occupancy states. Here, we use simulations to illuminate the inadequacies of modelling species interactions solely as a function of occupancy, as is common practice in ecology. We demonstrate erroneous inference into species interactions due to bias in parameter estimates when considering species occupancy alone. To address this critical issue, we propose, develop, and demonstrate an occupancy-abundance model designed explicitly for modelling abundance-mediated species interactions involving two or more species. When modelling interactions as a function of abundance rather than occupancy, we uncover previously unidentified interactions. Through an empirical case study and comprehensive simulations, we demonstrate the importance of accountin..., In the case study using empirical data, we examine the intraguild interactions between three carnivores, a top mesopredator in the system, the coyote, an intermediate mesopredator, the fisher, and a small carnivore, the American marten. There is a long history of examining intraguild interactions between fisher and marten through harvest (e.g., Hardy, 1907; Krohn, Zielinski, & Boone, 1997). Recent harvest-based evidence was used to infer negative interactions between all three species, with fishers being limited through intraguild killing by coyotes, and martens being limited by both fisher and coyotes (Jensen & Humphries, 2019). Nonetheless, the three species co-occur over much of the marten’s limited range in New York State and recent analysis using Rota et al. (2016) co-occurrence models was inconsistent with previous hypotheses. This analysis found fisher occupancy was higher conditional on coyote presence, and marten occurred independently from both other species (Twining e..., , # Abundance-mediated species interactions

# Summary

These are MCMC samplers, data simulators, and processing and run scripts for a occupancy-abundance model for abundance-mediated species interactions with a full example case study. This model framework models detection/non-detection data to estimated occupancy, abundance, and interactions between the species of interest. This model enables the user to apply summarized detection/non-detection data collected over repeat surveys to model interactions as a function of abundance. These samplers are presented in Twining et al. 2024, and are based on adaptations of the [Waddle et al. (2010)](https://www.jstor.org/stable/25680391) formulation for modelling species interactions within an occupancy model, but instead of modelling the state model of a subordinate species a function of the occupancy states, it is modelled as a function of abundance (N). We provide a range of MCMC samplers for different ecological scenarios between two or more sp...