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Welcome to uHMM R package

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What is uHMM ?

uHMM is a R package intended to construct an Unsupervised Hidden Markov Model

This software is a willingness of the 3 partners, ULCO/LISIC, AEAP and IFREMER/LER-BL, to provide the work resulting from the JSTARS 2015 publication to expert and non-expert users (in biology, numerical ecology and classification).

Keywords: Unsupervised learning - Hidden Markov Model - Spectral clustering - Harmful algal blooms - Application to phytoplankton.


The uHMM tool has already been used to detect:

  • phytoplankton blooms from data from fixed stations or floats: MAREL-Carnot, MAREL-Iroise/Molène, MAREL-MesuRho.
  • environmental zones from a Pocket Ferrybox (PFB, AOA) onboard the Eastern Channel.
  • Kévin Rousseeuw, Emilie Poisson Caillault, Alain Lefebvre, Denis Hamad. Hybrid Hidden Markov Model for Marine Environment Monitoring. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, IEEE, 2015, 8 (1), pp.204-213. <10.1109/JSTARS.2014.2341219>. PDF here
  • Modélisation de signaux temporels hautes fréquences multicapteurs à valeurs manquantes : Application à la prédiction des efflorescences phytoplanctoniques dans les rivières et les écosystèmes marins côtiers . Doctoral thesis manuscript of Kévin Rousseeuw under the supervision of Emilie Poisson Caillault, Alain Lefevbre and Denis Hamad. Defended on December 11, 2014 at the Université du Littoral Côte d'Opale. PDF here

Relateds projects

  • Convention ULCO/LISIC, IFREMER, Agence de l'eau artois Picardie : Co-funding of Kevin Rousseeuw's thesis, valorization of associated tools.
  • CPER MARCO : CPER 2014-2020, State-Region Plan Contract, between the State and the Hauts-de-France Region. Establishment of instruments and tools (surveys, indicators) for a global approach to the study of the marine environment, the resource and the quality of marine products.
  • JERICO-Next H2020 : Joint European Research Infrastructure Network for Coastal Observatories to reinforce and expand a strong and transparent European Network in the provision of operational services for the timely, continuous and sustainable delivery of high quality environmental data and information products related to the marine environment in the European coastal seas.

Contact us at emilie[dot]poisson[at]univ[-]littoral[dot]fr