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Background

overview

Hooke is implemented using the PLNmodels package. PLN models are a multivariate mixed generalized linear model with a Poisson distribution, allowing them to overcome the computational challenges posed by count data. They provide a convenient framework to perform multivariate statistical regression to describe how environmental effects or perturbations alter the relative abundances of each species.

References

  1. J. Chiquet, M. Mariadassou and S. Robin: The Poisson-lognormal model as a versatile framework for the joint analysis of species abundances, Frontiers in Ecology and Evolution, 2021.

  2. J. Chiquet, M. Mariadassou and S. Robin: Variational inference for sparse network reconstruction from count data, Proceedings of the 36th International Conference on Machine Learning (ICML), 2019.

  3. J. Chiquet, M. Mariadassou and S. Robin: Variational inference for probabilistic Poisson PCA, the Annals of Applied Statistics, 12: 2674–2698, 2018.