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Getting Things in Order: An Introduction to the R Package seriation

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  • Hahsler, Michael
  • Hornik, Kurt
  • Buchta, Christian

Abstract

Seriation, i.e., finding a suitable linear order for a set of objects given data and a loss or merit function, is a basic problem in data analysis. Caused by the problem's combinatorial nature, it is hard to solve for all but very small sets. Nevertheless, both exact solution methods and heuristics are available. In this paper we present the package seriation which provides an infrastructure for seriation with R. The infrastructure comprises data structures to represent linear orders as permutation vectors, a wide array of seriation methods using a consistent interface, a method to calculate the value of various loss and merit functions, and several visualization techniques which build on seriation. To illustrate how easily the package can be applied for a variety of applications, a comprehensive collection of examples is presented.

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  • Hahsler, Michael & Hornik, Kurt & Buchta, Christian, 2008. "Getting Things in Order: An Introduction to the R Package seriation," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 25(i03).
    • Handle: RePEc:jss:jstsof:v:025:i03
    DOI: http://hdl.handle.net/10.18637/jss.v025.i03
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    1. Niermann, Stefan, 2005. "Optimizing the Ordering of Tables With Evolutionary Computation," The American Statistician, American Statistical Association, vol. 59, pages 41-46, February.
    2. Dray, Stéphane & Dufour, Anne-Béatrice, 2007. "The ade4 Package: Implementing the Duality Diagram for Ecologists," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i04).
    3. Hahsler, Michael & Hornik, Kurt, 2007. "TSPInfrastructure for the Traveling Salesperson Problem," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 23(i02).
    4. Nathan Gale & William Halperin & C. Costanzo, 1984. "Unclassed matrix shading and optimal ordering in hierarchical cluster analysis," Journal of Classification, Springer;The Classification Society, vol. 1(1), pages 75-92, December.
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