Publications
Peer-reviewed papers
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. (2022)
“hmmTMB: Hidden Markov models with flexible covariate effects in R’
arXiv preprint, arXiv:2211.14139.
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.