Théo Michelot

School of Mathematics and Statistics
University of Sheffield
Hicks Building
Hounsfield Road
Sheffield S3 7RH


Hidden Markov models, and applications in ecology
Inference for stochastic differential equations
Animal movement models
Habitat selection models
Statistical software development


Since January 2016, I am a PhD student at the School of Mathematics and Statistics of the University of Sheffield, under the supervision of Paul Blackwell. I am working on incorporating more environmental information in statistical models of animal movement.
In 2015, I graduated from the Institut National des Sciences Appliquées of Rouen, in France, where I studied mathematics and computer science.
In 2013 and 2015, I spent some time at the Centre for Research into Ecological and Environmental Modelling of the University of St Andrews. There, I worked with Roland Langrock on the modelling of ecological data with hidden Markov models.

I am part of the group EcoHMM, which gathers researchers working on various ecological applications of hidden Markov models.

Publications and preprints

Google Scholar profile
Michelot, T., Blackwell, P.G., Matthiopoulos, J. (in press)
"Linking resource selection and step selection models for habitat preferences in animals"
Ecology. (Preprint: arXiv:1708.08426.)

Grecian, W.J., Lane, J., Michelot, T., Wade, H., Hamer, K.C. (in press)
"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, DOI: 10.1098/rsif.2018.0084.

McClintock, B., Michelot, T. (in press)
"momentuHMM: R package for generalized hidden Markov models of animal movement"
Methods in Ecology and Evolution, DOI: 10.1111/2041-210X.12995.

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.

Langrock, R., Kneib, T., Glennie, R., Michelot, T. (2017)
"Markov-switching generalized additive models"
Statistics and Computing. 27 (1), pp. 259-270.

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.

Michelot, T., Langrock, R., Kneib, T., King, R. (2016)
"Maximum penalized likelihood estimation in semiparametric capture-recapture models"
Biometrical Journal, 58, pp. 223-239.

Langrock, R., Michelot, T., Sohn, A., Kneib, T. (2015)
"Semiparametric stochastic volatility modelling using penalized splines"
Computational Statistics, 30, pp. 517-537.


Github profile
We developed the R package moveHMM for the analysis of movement data with hidden Markov models.
  • CRAN: description, documentation, archives...
  • Github: latest (unstable) version of the code.
  • Get started with the vignette. There, we describe the functionalities of the package in detail, and illustrate their use on elk tracking data.
  • Short video presentation for MEE.

The R package momentuHMM extends moveHMM to more general and flexible models. Additional features include: unlimited number of data streams, inclusion of covariates on the observation distribution parameters, centres of attraction, multiple imputation to account for irregular sampling and/or measurement error, etc.

I wrote a document about implementing hidden Markov models, which describes two examples in detail: a 2-state HMM with Poisson-distributed observations, and a 3-state HMM inspired by movement models. R code is provided for simulation, estimation, and inference in these models.

Talks and workshops

"moveHMM and momentuHMM -- Analysing animal movement in R"
Tutorial at the moving2gather meeting, Montpellier, France. December 2017.

"Can animals do MCMC? Linking resource selection and step selection models"
Poster at the Bio-logging symposium, Konstanz, Germany. September 2017.
Click to see my poster.

"Hidden Markov models for animal movement and other ecological data". Demonstrator.
Workshop held in St Andrews, UK. August 2017.

"From movement to space use"
Flash talk at the meeting of BES movement ecology group, London, UK. July 2017.

"momentuHMM: an R package for the analysis of general telemetry data using hidden Markov models"
Talk at the EURING meeting, Barcelona, Spain. July 2017.

"Can animals do MCMC? Integrating resource selection and step selection"
Talk at the meeting of the National Centre for Statistical Ecology, Canterbury, UK. June 2017.

"Analysing animal movement data with moveHMM -- Conservation action plan for the wild haggis"
Talk at the International Statistical Ecology Conference, Seattle, USA. June 2016.
Best student talk award.

"Multistate Ornstein-Uhlenbeck processes for modelling animal movement"
Talk at the Research Students' Conference in Probability and Statistics, Dublin, Ireland. June 2016.

"moveHMM: an R package for modelling animal movement with hidden Markov models"
Seminar at the Australian Antarctic Division, Hobart, Australia. June 2016.

"Hidden Markov models for animal movement and other ecological data". Demonstrator.
Workshop held in Mossel Bay, South Africa. March 2016.
Workshop report

"moveHMM: an R package for modelling animal movement with hidden Markov models"
Seminar at the Sea Mammal Research Unit, St Andrews, UK. November 2015.

"A statistical introduction to animal movement modelling"
Talk at the German Statistical Week, Hamburg, Germany. September 2015.