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EMMIXuskew: An R Package for Fitting Mixtures of Multivariate Skew t Distributions via the EM Algorithm

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  • McLachlan, Geoff
  • Lee, Sharon X

Abstract

This paper describes an algorithm for fitting finite mixtures of unrestricted Multivariate Skew t (FM-uMST) distributions. The package EMMIXuskew implements a closed-form expectation-maximization (EM) algorithm for computing the maximum likelihood (ML) estimates of the parameters for the (unrestricted) FM-MST model in R. EMMIXuskew also supports visualization of fitted contours in two and three dimensions, and random sample generation from a specified FM-uMST distribution. Finite mixtures of skew t distributions have proven to be useful in modelling heterogeneous data with asymmetric and heavy tail behaviour, for example, datasets from flow cytometry. In recent years, various versions of mixtures with multivariate skew t (MST) distributions have been proposed. However, these models adopted some restricted characterizations of the component MST distributions so that the E-step of the EM algorithm can be evaluated in closed form. This paper focuses on mixtures with unrestricted MST components, and describes an iterative algorithm for the computation of the ML estimates of its model parameters. Its implementation in R is presented with the package EMMIXuskew. The usefulness of the proposed algorithm is demonstrated in three applications to real datasets. The first example illustrates the use of the main function fmmst in the package by fitting a MST distribution to a bivariate unimodal flow cytometric sample. The second example fits a mixture of MST distributions to the Australian Institute of Sport (AIS) data, and demonstrates that EMMIXuskew can provide better clustering results than mixtures with restricted MST components. In the third example, EMMIXuskew is applied to classify cells in a trivariate flow cytometric dataset. Comparisons with some other available methods suggest that EMMIXuskew achieves a lower misclassification rate with respect to the labels given by benchmark gating analysis.

Suggested Citation

  • McLachlan, Geoff & Lee, Sharon X, 2013. "EMMIXuskew: An R Package for Fitting Mixtures of Multivariate Skew t Distributions via the EM Algorithm," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 55(i12).
    • Handle: RePEc:jss:jstsof:v:055:i12
    DOI: http://hdl.handle.net/10.18637/jss.v055.i12
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    References listed on IDEAS

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    2. Badi H. Baltagi & Georges Bresson & Anoop Chaturvedi & Guy Lacroix, 2021. "Robust Dynamic Panel Data Models Using 𝛆𝛆-Contamination," Center for Policy Research Working Papers 240, Center for Policy Research, Maxwell School, Syracuse University.
    3. Rachid Laajaj & Duncan Webb & Danilo Aristizabal & Eduardo Behrentz & Raquel Bernal & Giancarlo Buitrago & Zulma Cucunubá & Fernando de la Hoz, 2021. "Understanding how socioeconomic inequalities drive inequalities in SARS-CoV-2 infections," Documentos CEDE 19241, Universidad de los Andes, Facultad de Economía, CEDE.
    4. Wan-Lun Wang & Ahad Jamalizadeh & Tsung-I Lin, 2020. "Finite mixtures of multivariate scale-shape mixtures of skew-normal distributions," Statistical Papers, Springer, vol. 61(6), pages 2643-2670, December.
    5. Lee, Sharon X. & McLachlan, Geoffrey J., 2022. "An overview of skew distributions in model-based clustering," Journal of Multivariate Analysis, Elsevier, vol. 188(C).
    6. Lin, Tsung-I & McLachlan, Geoffrey J. & Lee, Sharon X., 2016. "Extending mixtures of factor models using the restricted multivariate skew-normal distribution," Journal of Multivariate Analysis, Elsevier, vol. 143(C), pages 398-413.
    7. Ahad Jamalizadeh & Tsung-I Lin, 2017. "A general class of scale-shape mixtures of skew-normal distributions: properties and estimation," Computational Statistics, Springer, vol. 32(2), pages 451-474, June.
    8. José E. Chacón, 2019. "Mixture model modal clustering," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 13(2), pages 379-404, June.
    9. Baltagi, Badi H. & Bresson, Georges & Chaturvedi, Anoop & Lacroix, Guy, 2022. "Robust Dynamic Space-Time Panel Data Models Using ?-Contamination: An Application to Crop Yields and Climate Change," IZA Discussion Papers 15815, Institute of Labor Economics (IZA).
    10. Antonio Parisi & B. Liseo, 2018. "Objective Bayesian analysis for the multivariate skew-t model," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 27(2), pages 277-295, June.
    11. Murray, Paula M. & Browne, Ryan P. & McNicholas, Paul D., 2017. "Hidden truncation hyperbolic distributions, finite mixtures thereof, and their application for clustering," Journal of Multivariate Analysis, Elsevier, vol. 161(C), pages 141-156.
    12. McLachlan, Geoffrey J. & Lee, Sharon X., 2016. "Comment on “On nomenclature, and the relative merits of two formulations of skew distributions” by A. Azzalini, R. Browne, M. Genton, and P. McNicholas," Statistics & Probability Letters, Elsevier, vol. 116(C), pages 1-5.
    13. Wraith, Darren & Forbes, Florence, 2015. "Location and scale mixtures of Gaussians with flexible tail behaviour: Properties, inference and application to multivariate clustering," Computational Statistics & Data Analysis, Elsevier, vol. 90(C), pages 61-73.
    14. Azzalini, Adelchi & Browne, Ryan P. & Genton, Marc G. & McNicholas, Paul D., 2016. "On nomenclature for, and the relative merits of, two formulations of skew distributions," Statistics & Probability Letters, Elsevier, vol. 110(C), pages 201-206.

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