Provide functions to make estimate the number of states for a hidden Markov 
    model (HMM) using marginal likelihood method proposed by the authors.
    See the Manual.pdf file a detail description of all functions, and a detail tutorial.

Analysing time-series accelerometer data to quantify length and 
             intensity of physical activity using hidden Markov models. 
             It also contains the traditional cut-off point method.
             Witowski V, Foraita R, Pitsiladis Y, Pigeot I, Wirsik N (2014).
             <doi:10.1371/journal.pone.0114089>.

Datasets and code examples that accompany our book Visser & Speekenbrink (2021), "Mixture and Hidden Markov Models with R", <https://depmix.github.io/hmmr/>.

Reliability Analysis and Maintenance Optimization using Hidden Markov Models (HMM). The use of HMMs to model the state of a system which is not directly observable and instead certain indicators (signals) of the true situation are provided via a control system. A hidden model can provide key information about the system dependability, such as the reliability of the system and related measures. An estimation procedure is implemented based on the Baum-Welch algorithm. Classical structures such as K-out-of-N systems and Shock models are illustrated. Finally, the maintenance of the system is considered in the HMM context and two functions for new preventive maintenance strategies are considered. Maintenance efficiency is measured in terms of expected cost. Methods are described in Gamiz, Limnios, and Segovia-Garcia (2023) <doi:10.1016/j.ejor.2022.05.006>.

Fitting hidden Markov models using automatic differentiation 
  and Laplace approximation, allowing for fast inference and flexible covariate
  effects (including random effects and smoothing splines) on model parameters.
  The package is described by Michelot (2025) <doi:10.18637/jss.v114.i05>.

Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.