Biology subjects

Lavender, E.

Publications and source records attributed to Lavender, E..

4 recordsLinked to original sources

bioRxiv2025

Animal geolocation with convolution algorithms in Julia and R via Wahoo.jl

O_LIAnimal geolocation is the core of movement ecology. In aquatic ecosystems, electronic tagging and tracking technologies, such as passive acoustic telemetry systems and biologging sensors, are widely deployed. However, statistical estimation of individual locations from these datasets can be challenging and computationally expensive. C_LIO_LIHere, we introduce Wahoo.jl, a Julia package that fits state-space models to animal-tracking data via convolution algorithms. Wahoo.jl supports passive acoustic telemetry (detection/non-detection) and biologging (i.e., depth) datasets; implements grid-based filtering, smoothing and sampling of trajectories; and exploits GPU acceleration. C_LIO_LIUsing simulations, we illustrate how to use Wahoo.jl from Julia and R to reconstruct movements for an example individual tagged with an acoustic transmitter and an archival depth tag. We also provide validation and sensitivity analyses. C_LIO_LIWahoo.jl fills a key gap in the animal-tracking toolbox. The package provides an accessible, flexible and performant interface for an inference methodology that reliably handles multimodal inference problems that challenge other approaches. We discuss the approachs pros and cons and provide guidance to readers on when to reach for Wahoo.jl. C_LI

ecology↗

bioRxiv2025

Animal tracking with particle algorithms for conservation

The movements of aquatic animals affect their exposure to threats and the efficacy of conservation measures, such as Marine Protected Areas (MPAs). However, many species movements remain poorly understood and difficult to reconstruct from available datasets, hampering conservation efforts. This is especially the case for species that rarely surface, for which data are often limited to observations from acoustic telemetry (detections) and ancillary sensors, such as archival tags. Here, we pioneer the use of state-of-the-art particle algorithms to model animal movement, integrate datasets and assess MPA design, using a case study of the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. Our algorithms led to 5-fold improvements in maps of space use and 30-fold improvements in residency estimates (lower mean error) compared to prevailing heuristic methods. By formally integrating tracking datasets, we were uniquely able to examine movements beyond receivers into fished zones, MPA-scale residency and specific habitats beyond protected areas that may warrant protection. This work showcases a probabilistically sound modelling framework that is sufficiently fast, flexible and accessible to meet the demands of modern animal-tracking datasets in acoustic telemetry systems. This represents a marked advance for analyses of animal movements and MPA efficacy worldwide.

ecology↗

bioRxiv2024

Particle algorithms for animal movement modelling in autonomous receiver networks

1. Particle filters and smoothers are powerful sequential Monte Carlo algorithms used to fit non-linear, non-Gaussian state-space models. These algorithms are well placed to fit process-orientated models to animal-tracking data, especially in autonomous receiver networks, but to date they have received limited attention in the ecological literature. 2. Here, we introduce a Bayesian filtering-smoothing algorithm that reconstructs individual movements and patterns of space use from animal-tracking data, with a focus on passive acoustic telemetry systems. Within a sound probabilistic framework, the methodology uniquely integrates the movement process and the observation processes of disparate datasets, while correctly representing uncertainty. In a comprehensive simulation-based analysis, we compare the performance of our algorithm to the prevailing, heuristic methods used in passive acoustic telemetry systems and analyse algorithm sensitivity. 3. We find the particle smoothing methodology outperforms heuristic methods across the board. Particle-based maps consistently represent simulated movements more accurately, even in dense receiver networks, and are better suited to analyses of home ranges, residency and habitat preferences. 4. This study sets a new state-of-the-art for movement modelling in autonomous receiver networks. Particle algorithms provide a flexible and intuitive modelling framework with potential applications in many ecological settings.

animal behavior and cognition↗

bioRxiv2024

patter: particle algorithms for animal tracking in R and Julia

O_LIIn the field of movement ecology, state-space models have emerged as a powerful modelling framework that represents individual movements and the processes that connect movements to observations. However, fitting state-space models to animal tracking data is often difficult and computationally expensive. C_LIO_LIHere, we introduce patter, a package that provides particle filtering and smoothing algorithms that fit Bayesian state-space models to tracking data, with a focus on data from aquatic animals in autonomous receiver arrays. patter is written in R, with a high-performance Julia backend. Package functionality supports data simulation, preparation, filtering, smoothing and mapping. C_LIO_LIIn two worked examples, we demonstrate how to implement patter to reconstruct the movements of a tagged animal in an acoustic telemetry system from acoustic detections and ancillary observations. With perfect information, the particle filter reconstructs the true (unobserved) movement path (Example One). More generally, particle-based methods represent an individuals possible location probabilistically as a weighted series of samples ( particles). In our illustration, we resolve an individuals (unobserved) location every two minutes during one month in minutes and use particles to visualise movements, map space use and quantify residency (Example Two). C_LIO_LIpatter facilitates robust, flexible and efficient analyses of animal tracking data. The methods are widely applicable and enable refined analyses of home ranges, residency and habitat preferences. C_LI

ecology↗