arXiv subjects

Fanny Dupont

Publications and source records attributed to Fanny Dupont.

4 recordsLinked to original sources

arXiv2026

Inferring resource selection and utilization distributions from irregular and error-prone animal tracking data

Habitat selection and space use are fundamental to understanding animal distribution. Traditional methods for quantifying habitat preferences from telemetry data assume regular sampling and negligible measurement error. However, these assumptions are routinely violated in marine systems. Practitioners typically regularize and filter the data before fitting models, but these two-step procedures do not propagate uncertainty from the filtering stage and can yield biased estimates. Habitat-driven Langevin diffusion models offer an elegant alternative, naturally accommodating irregular sampling. However, incorporating measurement error via a state-space formulation is challenging because habitat covariates depend on the latent true locations. We address this using the Laplace approximation to simultaneously integrate over true locations and account for habitat covariates along latent paths, yielding a single-stage framework efficiently implemented in Template Model Builder (TMB). By doing so, we provide the first TMB implementation capable of handling covariates that depend on latent variables, allowing inference via fast and efficient maximum likelihood estimation. Simulations show that our approach outperforms the two-step method, recovering habitat-selection parameters even under substantial measurement error and missing data, with more accurate utilization distributions and trajectory reconstructions. Applied to narwhal (Monodon monoceros) telemetry data, the two-step method substantially shrinks the habitat selection coefficient towards zero, while our unified approach recovers a much stronger signal. Our framework offers a computationally efficient solution to long-standing challenges of measurement error and temporal irregularity in habitat selection inference, applicable across a wide range of taxa and environments.

stat.ME↗

arXiv2026

Estimating the distance at which narwhal respond to disturbance: a penalized threshold hidden Markov model

Understanding behavioural responses to disturbances is vital for wildlife conservation. For example, in the Arctic, the decrease in sea ice has opened new shipping routes, increasing the need for impact assessments that quantify the distance at which marine mammals react to vessel presence. This information can then guide targeted mitigation policies, such as vessel slow-down regulations and delineation of avoidance areas. Using telemetry data to determine distances linked to deviations from normal behaviour requires advanced statistical models, such as threshold hidden Markov models (THMMs). While these are powerful tools, they do not assess whether the estimated threshold reflects a meaningful behavioural shift. We introduce a lasso-penalized THMM that builds on computationally efficient methods to impose penalties on HMMs and present a new, efficient penalized quasi-restricted maximum-likelihood estimator. Our framework is capable of estimating thresholds and assessing whether the disturbance effects are distinguishable from baseline behaviour. With simulations, we demonstrate that our lasso method effectively shrinks spurious threshold effects towards zero. When applied to narwhal movement data, our analysis suggests that narwhal react to vessels up to 3.4 kilometres away by decreasing movement persistence and spending more time in deeper waters (average maximum depth of 356m). Overall, we provide a broadly applicable framework for quantifying behavioural responses to stimuli, with applications ranging from determining reaction thresholds to disturbance to estimating the distances at which terrestrial species, such as elephants, detect water. We also provide a tutorial and an open-source implementation to facilitate the application of our framework.

stat.AP↗

arXiv2025

Flexible unimodal density estimation in hidden Markov models

1. Hidden Markov models (HMMs) are powerful tools for modelling time-series data with underlying state structure. However, selecting appropriate parametric forms for the state-dependent distributions is often challenging and can lead to model misspecification. To address this, P-spline-based nonparametric estimation of state-dependent densities has been proposed. While offering great flexibility, these approaches can result in overly complex densities (e.g. bimodal) that hinder interpretability. 2. We propose a straightforward method that builds on shape-constrained spline theory to enforce unimodality in the estimated state-dependent densities through enforcing unimodality of the spline coefficients. This constraint strikes a practical balance between model flexibility, interpretability, and parsimony. 3. Through two simulation studies and a real-world case study using narwhal (Monodon monoceros) dive data, we demonstrate the proposed approach yields more stable estimates compared to fully flexible, unconstrained models improving model performance and interpretability. 4. Our method bridges a key methodological gap, by providing a parsimonious HMM framework that balances the interpretability of parametric models with the flexibility of nonparametric estimation. This provides ecologists with a powerful tool to derive ecologically meaningful inference from telemetry data while avoiding the pitfalls of overly complex models.

stat.ME↗

arXiv2024

Improved order selection method for hidden Markov models: a case study with movement data

Hidden Markov models (HMMs) are a versatile statistical framework commonly used in ecology to characterize behavioural patterns from animal movement data. In HMMs, the observed data depend on a finite number of underlying hidden states, generally interpreted as the animal's unobserved behaviour. The number of states is a crucial parameter, controlling the trade-off between ecological interpretability of behaviours (fewer states) and the goodness of fit of the model (more states). Selecting the number of states, commonly referred to as order selection, is notoriously challenging. Common model selection metrics, such as AIC and BIC, often perform poorly in determining the number of states, particularly when models are misspecified. Building on existing methods for HMMs and mixture models, we propose a double penalized likelihood maximum estimate (DPMLE) for the simultaneous estimation of the number of states and parameters of non-stationary HMMs. The DPMLE differs from traditional information criteria by using two penalty functions on the stationary probabilities and state-dependent parameters. For non-stationary HMMs, forward and backward probabilities are used to approximate stationary probabilities. Using a simulation study that includes scenarios with additional complexity in the data, we compare the performance of our method with that of AIC and BIC. We also illustrate how the DPMLE differs from AIC and BIC using narwhal (Monodon monoceros) movement data. The proposed method outperformed AIC and BIC in identifying the correct number of states under model misspecification. Furthermore, its capacity to handle non-stationary dynamics allowed for more realistic modeling of complex movement data, offering deeper insights into narwhal behaviour. Our method is a powerful tool for order selection in non-stationary HMMs, with potential applications extending beyond the field of ecology.

stat.ME↗