Publications

Peer-reviewed papers

Santos Neto, C., Dwyer, R., Michelot, T., Cristescu, R. (in press).
“Effects of urbanisation on the movements of an arboreal specialist using hidden Markov models”
Movement Ecology.

Michelot, T. (2025).
“hmmTMB: hidden Markov models with flexible covariate effects in R”
Journal of Statistical Software, 114(5), pp. 1-45.
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Klappstein, N.J., Michelot, T., Fieberg, J., Pedersen, E.J., & Mills Flemming, J. (2024).
“Step selection functions with non‐linear and random effects”
Methods in Ecology and Evolution, 15(8), pp. 1332-1346.
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Invernizzi, E., Michelot, T., Popov, V., Ng, N., Macqueen, E., Rouviere, A., … & Sasaki, T. (2024).
“Identifying cues for self-organized nest wall-building behaviour in the rock ant, Temnothorax rugatulus, using hidden Markov models”
Animal Behaviour, 210, pp. 315-330.
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Michelot, T., Klappstein, N. J., Potts, J. R., & Fieberg, J. (2024).
“Understanding step selection analysis through numerical integration”
Methods in Ecology and Evolution, 15(1), pp. 24-35.
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Michelot, T., Glennie, R., Thomas, L., Quick, N., Harris, C.M. (2023)
“Continuous-time modelling of behavioural responses in animal movement”
Annals of Applied Statistics, 17 (4), pp. 3570-3588.
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Klappstein, N.J., Thomas, L., & Michelot, T. (2023)
“Flexible hidden Markov models for behaviour-dependent habitat selection”
Movement Ecology, 11 (30), DOI: 10.1186/s40462-023-00392-3.
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Glennie, R., Adam, T., Leos-Barajas, V., Michelot, T., Photopoulou, T., & McClintock, B.T. (2023)
“Hidden Markov models: pitfalls and opportunities in ecology”
Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.13801.
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Klappstein, N.J., Potts, J.R., Michelot, T., Börger, L., Pilfold, N.W., Lewis, M., Derocher, A.E. (2022)
“Energy-based step selection analysis: modelling the energetic drivers of animal movement and habitat use”
Journal of Animal Ecology, DOI: 10.1111/1365-2656.13687.
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Michelot, T., Glennie, R., Harris, C., Thomas, L. (2021)
“Varying-coefficient stochastic differential equations with applications in ecology”
Journal of Agricultural, Biological, and Environmental Statistics. DOI: 10.1007/s13253-021-00450-6.
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Conners, M., Michelot, T., Heywood, E., Orben, R.A., Phillips, R., Vyssotski, A., Shaffer, S.A., Thorne, L. (2021)
“Hidden Markov models reveal major animal movement modes from multi-sensor tags: a case study of four albatross species”
Movement Ecology, 9 (7), DOI: 10.1186/s40462-021-00243-z.
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Runde, B.J., Michelot, T., Bacheler, N.M., Shertzer, K.W. and Buckel, J.A. (2020)
“Assigning fates in telemetry studies using hidden Markov models: an application to deepwater groupers released with descender devices”
North American Journal of Fisheries Management, 40, pp. 1417-1434.
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Michelot, T., Blackwell, P.G., Chamaillé-Jammes, S., Matthiopoulos, J. (2020)
“Inference in MCMC step selection models”
Biometrics, 76, pp. 438-447.
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Farhadinia, M.S., Michelot, T., Johnson, P.J., Hunter, L.T.B., MacDonald, D.W. (2020)
“Understanding decision making in a food-caching predator using hidden Markov models”
Movement Ecology, 8 (9), DOI: 10.1186/s40462-020-0195-z.
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Spangenberg, M.C., Serrouya, R., Dickie, M., DeMars, C.A., Michelot, T., Boutin, S., and Wittmann, M.J. (2019)
“Slowing down wolves to protect boreal caribou populations: a spatial simulation model of linear feature restoration”
Ecosphere, 10 (10), DOI: 10.1002/ecs2.2904.
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Michelot, T., Étienne, M.P., Gloaguen, P., Blackwell, P.G. (2019)
“The Langevin diffusion as a continuous-time model of animal movement and habitat selection”
Methods in Ecology and Evolution, 10 (11), pp. 1894-1907.
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Michelot, T., Blackwell, P.G. (2019)
“State-switching continuous-time correlated random walks”
Methods in Ecology and Evolution, 10 (5), pp. 637-649.
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Bacheler, N. M., Michelot, T., Cheshire, R. T., Shertzer, K. W. (2019)
“Fine-scale movement patterns and behavioral states of gray triggerfish Balistes capriscus determined from acoustic telemetry and hidden Markov models”
Fisheries Research, 215, pp. 76-89.
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Michelot, T., Blackwell, P.G., Matthiopoulos, J. (2019)
“Linking resource selection and step selection models for habitat preferences in animals”
Ecology, 100 (1), DOI: 10.1002/ecy.2452.
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Grecian, W.J., Lane, J., Michelot, T., Wade, H., Hamer, K.C. (2018)
“Understanding the ontogeny of foraging behaviour: insights from combining marine predator bio-logging with satellite-derived oceanography in hidden Markov models”
Journal of the Royal Society Interface, 15 (143), DOI: 10.1098/rsif.2018.0084.
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McClintock, B., Michelot, T. (2018)
“momentuHMM: R package for generalized hidden Markov models of animal movement”
Methods in Ecology and Evolution, 9 (6), pp. 1518-1530.
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Michelot, T., Langrock, R., Bestley, S., Jonsen, I.D., Photopoulou, T., Patterson, T.A. (2017)
“Estimation and simulation of foraging trips in land-based marine predators”
Ecology, 98 (7), pp. 1932-1944.
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Langrock, R., Kneib, T., Glennie, R., Michelot, T. (2017)
“Markov-switching generalized additive models”
Statistics and Computing, 27 (1), pp. 259-270.
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Michelot, T., Langrock, R., Patterson, T.A. (2016)
“moveHMM: an R package for analysing animal movement data using hidden Markov models”
Methods in Ecology and Evolution, 7 (11), pp. 1308-1315.
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Michelot, T., Langrock, R., Kneib, T., King, R. (2016)
“Maximum penalized likelihood estimation in semiparametric capture-recapture models”
Biometrical Journal, 58, pp. 223-239.
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Langrock, R., Michelot, T., Sohn, A., Kneib, T. (2015)
“Semiparametric stochastic volatility modelling using penalized splines”
Computational Statistics, 30, pp. 517-537.
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Preprints

Michelot, T. (2024)
“Multiscale modelling of animal movement with persistent dynamics”
arXiv preprint, arXiv:2406.15195.

Leos-Barajas, V., Michelot, T. (2018)
“An introduction to animal movement modeling with hidden Markov models using Stan for Bayesian inference”
arXiv preprint, arXiv:1806.10639.

Book chapters

Antinori, P., Michelot, T., Lescuyer, P., Müller, M., Acosta-Martin, A.E. (2019)
“Detection of unknown chemical adduct modifications on proteins: from wet to dry laboratory”
In: Mass Spectrometry of Proteins (pp. 99-113). Humana Press, New York, NY.