To cite the funHMM package or the methodology in publications use:

  Kashlak, A. B., Loliencar, P. and Heo, G. (2023). Topological Hidden
  Markov Models. Journal of Machine Learning Research, 24(340), 1-49.
  https://jmlr.org/papers/v24/22-0685.html

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Topological Hidden Markov Models},
    author = {Adam B Kashlak and Prachi Loliencar and Giseon Heo},
    journal = {Journal of Machine Learning Research},
    year = {2023},
    volume = {24},
    number = {340},
    pages = {1--49},
    url = {https://jmlr.org/papers/v24/22-0685.html},
  }