Hidden Markov Modelling (HMM)

Published

November 28, 2025

Packages

moveHMM - https://cran.r-project.org/web/packages/moveHMM/vignettes/moveHMM-guide.pdf - For fitting hidden Markov models to animal movement data
momentuHMM - https://cran.r-project.org/web/packages/momentuHMM/vignettes/momentuHMM.pdf - Essentially an updated version of moveHMM with more flexibility

Tutorials and resources

`moveHMM` package documentation and tutorials

https://cran.r-project.org/web/packages/moveHMM/vignettes/moveHMM-guide.pdf
Michelot, T., Langrock, R., & Patterson, T. A. (2016). moveHMM: an R package for the statistical modelling of animal movement data using hidden Markov models. Methods in Ecology and Evolution, 7(11), 1308–1315. https://doi.org/10.1111/2041-210X.12578

`momentuHMM` package documentation and tutorials

https://cran.r-project.org/web/packages/momentuHMM/vignettes/momentuHMM.pdf
McClintock, B. T., & Michelot, T. (2018). momentuHMM: R package for generalized hidden Markov models of animal movement. Methods in Ecology and Evolution, 9(6), 1518–1530. https://doi.org/10.1111/2041-210X.12995

HMM tutorial

https://mjones029.github.io/Tutorials/HMM_tutorial.html

Behavioral Analysis in R - includes both HMMs and Behavioural Change Point Analysis (BCPA)

https://www.danaseidel.com/MovEco-R-Workshop/Materials/Day6/Behavioral_Analysis/

Useful papers

(Langrock et al. 2012) - Langrock, R., King, R., Matthiopoulos, J., Thomas, L., Fortin, D., & Morales, J. M. (2012). Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions. Ecology, 93(11), 2336–2342. https://doi.org/10.1890/11-2241.1

(Pohle et al. 2017) - Pohle, J., Langrock, R., van Beest, F. M., & Schmidt, N. M. (2017). Selecting the Number of States in Hidden Markov Models: Pragmatic Solutions Illustrated Using Animal Movement. Journal of Agricultural, Biological, and Environmental Statistics, 22(3), 270–293. https://doi.org/10.1007/s13253-017-0283-8

References

Langrock, Roland, Ruth King, Jason Matthiopoulos, Len Thomas, Daniel Fortin, and Juan M Morales. 2012. “Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions.” Ecology 93 (November): 2336–42. https://doi.org/10.1890/11-2241.1.

Pohle, Jennifer, Roland Langrock, Floris M van Beest, and Niels Martin Schmidt. 2017. “Selecting the Number of States in Hidden Markov Models: Pragmatic Solutions Illustrated Using Animal Movement.” Journal of Agricultural, Biological, and Environmental Statistics 22 (September): 270–93. https://doi.org/10.1007/s13253-017-0283-8.

--- title: "Hidden Markov Modelling (HMM)" # author: # - name: "Scott Forrest" # url: https://swforrest.github.io/ # orcid: 0000-0001-9529-0108 # affiliation: Queensland University of Technology, CSIRO # email: "scottwforrest@gmail.com" date: today execute: cache: false bibliography: ../paperpile_references.bib toc: true number-sections: false format: html: self-contained: true code-fold: show code-tools: true df-print: paged code-line-numbers: true code-overflow: scroll fig-format: png fig-dpi: 300 pdf: geometry: - top=30mm - left=30mm editor: source abstract: | --- ## Packages - `moveHMM` - <https://cran.r-project.org/web/packages/moveHMM/vignettes/moveHMM-guide.pdf> - For fitting hidden Markov models to animal movement data - `momentuHMM` - <https://cran.r-project.org/web/packages/momentuHMM/vignettes/momentuHMM.pdf> - Essentially an updated version of moveHMM with more flexibility ## Tutorials and resources #### `moveHMM` **package documentation and tutorials** - <https://cran.r-project.org/web/packages/moveHMM/vignettes/moveHMM-guide.pdf> - Michelot, T., Langrock, R., & Patterson, T. A. (2016). **moveHMM: an R package for the statistical modelling of animal movement data using hidden Markov models**. Methods in Ecology and Evolution, 7(11), 1308–1315. https://doi.org/10.1111/2041-210X.12578 #### `momentuHMM` **package documentation and tutorials** - <https://cran.r-project.org/web/packages/momentuHMM/vignettes/momentuHMM.pdf> - McClintock, B. T., & Michelot, T. (2018). **momentuHMM: R package for generalized hidden Markov models of animal movement**. Methods in Ecology and Evolution, 9(6), 1518–1530. https://doi.org/10.1111/2041-210X.12995 #### HMM tutorial - <https://mjones029.github.io/Tutorials/HMM_tutorial.html> #### Behavioral Analysis in R - *includes both HMMs and Behavioural Change Point Analysis (BCPA)* - <https://www.danaseidel.com/MovEco-R-Workshop/Materials/Day6/Behavioral_Analysis/> ## Useful papers [@Langrock2012-yu] - Langrock, R., King, R., Matthiopoulos, J., Thomas, L., Fortin, D., & Morales, J. M. (2012). **Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions**. Ecology, 93(11), 2336–2342. https://doi.org/10.1890/11-2241.1 [@Pohle2017-rb] - Pohle, J., Langrock, R., van Beest, F. M., & Schmidt, N. M. (2017). **Selecting the Number of States in Hidden Markov Models: Pragmatic Solutions Illustrated Using Animal Movement**. Journal of Agricultural, Biological, and Environmental Statistics, 22(3), 270–293. https://doi.org/10.1007/s13253-017-0283-8 # References ::: {#refs} :::