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Implementing a Class of Permutation Tests: The coin Package

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  • Hothorn, Torsten
  • Hornik, Kurt
  • van de Wiel, Mark A.
  • Zeileis, Achim

Abstract

The R package coin implements a unified approach to permutation tests providing a huge class of independence tests for nominal, ordered, numeric, and censored data as well as multivariate data at mixed scales. Based on a rich and flexible conceptual framework that embeds different permutation test procedures into a common theory, a computational framework is established in coin that likewise embeds the corresponding R functionality in a common S4 class structure with associated generic functions. As a consequence, the computational tools in coin inherit the flexibility of the underlying theory and conditional inference functions for important special cases can be set up easily. Conditional versions of classical tests---such as tests for location and scale problems in two or more samples, independence in two- or three-way contingency tables, or association problems for censored, ordered categorical or multivariate data---can easily be implemented as special cases using this computational toolbox by choosing appropriate transformations of the observations. The paper gives a detailed exposition of both the internal structure of the package and the provided user interfaces along with examples on how to extend the implemented functionality.

Suggested Citation

  • Hothorn, Torsten & Hornik, Kurt & van de Wiel, Mark A. & Zeileis, Achim, 2008. "Implementing a Class of Permutation Tests: The coin Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 28(i08).
    • Handle: RePEc:jss:jstsof:v:028:i08
    DOI: http://hdl.handle.net/10.18637/jss.v028.i08
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    References listed on IDEAS

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    1. Hothorn, Torsten & Hornik, Kurt & van de Wiel, Mark A. & Zeileis, Achim, 2006. "A Lego System for Conditional Inference," The American Statistician, American Statistical Association, vol. 60, pages 257-263, August.
    2. Meyer, David & Zeileis, Achim & Hornik, Kurt, 2006. "The Strucplot Framework: Visualizing Multi-way Contingency Tables with vcd," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 17(i03).
    3. Oster R.A., 2002. "An Examination of Statistical Software Packages for Categorical Data Analysis Using Exact Methods," The American Statistician, American Statistical Association, vol. 56, pages 235-246, August.
    4. Oster R.A., 2003. "An Examination of Statistical Software Packages for Categorical Data Analysis Using Exact Methods-Part II," The American Statistician, American Statistical Association, vol. 57, pages 201-213, August.
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