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Review of HSMM R and Python softwares

Bérard C., Cros M.J., Durand J.B., Lothodé C., Plancade S., Trepos R., Vergne N.. 2025. In : Peyrard Nathalie (ed.), De Saporta Benoîte (ed.). A comprehensive guide to HSMM: Theory, software, and advanced extensions. Londres : ISTE; John Wiley, p. 47-77. (Mathematics and Statistics Series / ISTE).

DOI: 10.1002/9781394427581.ch2

This chapter provides a comprehensive review of the various software and packages available for hidden semi-Markov models (HSMMs) or with a particular focus on those related to the themes of this book: multichain models, coupled chains and the incorporation of covariates. It conducts a thorough survey to compile both R and Python packages that are specifically designed to handle HSMMs, along with those related to these key themes, although a significant lack of dedicated packages is identified in these thematic areas. The comparison of these packages is based on their functionalities, particularly in relation to the modeling of sojourn duration distributions and emission distributions for HSMMs. A Python package is applied to discrete emission distributions in the toy model Squirrel, while an R package is employed for continuous emission distributions in the toy model Deer.

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