Biology subjects

Mills, S. C.

Publications and source records attributed to Mills, S. C..

3 recordsLinked to original sources

bioRxiv2023

Introducing flocker: an R package for flexible occupancy modeling via brms and Stan

O_LIOccupancy models are a widespread tool for analyzing biological survey data, but packages for fitting these models offer a limited variety of effects structures. C_LIO_LIWe developed Rpackage flocker to connect occupancy models (single- and multi- species; single- and multi-season) to the uniquely powerful formula syntax of Rpackage brms. C_LIO_LIUsing familiar formula-based syntax, flocker models can readily incorporate a wide array of effects structures, including phylogenetic random effects, splines, Gaussian processes, autoregressive structures, monotonic effects, and nonlinear predictors. These are available for use in formulas for occupancy, detection, colonization, extinction, and autologistic terms (as applicable to the model type). flocker additionally provides functionality for data simulation, posterior prediction, and model comparison, following well-documented statistical decisions that we put forward as best practices. C_LIO_LIWe anticipate that flocker will facilitate the work of practitioners who seek added realism in occupancy models. We further hope that flockers synthesis of these models will help inform best practices around occupancy modeling. C_LI

ecology↗

bioRxiv2022

Validation of a novel fully immersive Virtual Reality setup with a behavioural study of freely-moving fish

Virtual Reality (VR) enables standardised stimuli to invoke behavioural responses in animals, however, in fish studies VR has been limited to either basic virtual stimulation projected below the bowl for freely-swimming individuals or a simple virtual arena rendered over a large field-of-view for head-restrained individuals. We developed a novel immersive VR setup with real-time rendering of animated 3D scenarios, validated in a proof of concept study on the behaviour of coral reef post-larval fish. Fish use a variety of cues to select a habitat during the recruitment stage, and to recognize conspecifics and predators, but which visual cues are used remains unknown. We measured behavioural responses of groups of five convict surgeonfish (Acanthurus triostegus) to simulations of habitats, static or moving shoals of conspecifics, predators, and non-aggressive heterospecifics. Post-larval fish were consistently attracted to virtual corals and conspecifics presented statically, but repulsed by their predators (bluefin jacks, Caranx melampygus). When simulated shoals passed nearby repeatedly, they were again attracted by conspecifics showing a tendency to follow the shoal, whereas they moved repeatedly to the back of the passing predator shoal. They also discriminated between species of similar sizes: they were attracted more to conspecifics than butterflyfish (Forcipiger longirostris), and repulsed more by predators than parrotfish (Scarus psittacus). The quality of visual simulations was high enough to identify between visual cues - size, body shape, colour pattern - used by post-larval fish in species recognition. Despite a tracking technology limited to fish 2D positions in the aquarium, preventing the real-time updating of the rendered viewpoint, we could show that VR and modern tracking technologies offer new possibilities to investigate fish behaviour through the quantitative analysis of their physical reactions to highly-controlled scenarios.

animal behavior and cognition↗

bioRxiv2021

Biogeographic multi-species occupancy models for large-scale survey data

O_LIEcologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi-species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local-scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously. C_LIO_LIWe show how this challenge can be overcome by incorporating pre-existing range information into MSOMs, yielding a biogeographic multi-species occupancy model (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey, and entire avian communities in forests and pastures of Colombias West Andes. C_LIO_LICompared to traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species-specific inference even for never-observed species. C_LIO_LIIncorporating pre-existing range data enables principled partial pooling of information across species in large-scale MSOMs. Our biogeographic framework for multi-species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false-absences are modeled in an occupancy framework. C_LI

ecology↗