Wednesday, January 28, 2009


  1. R:
    • Package: stats

    • Package: proxy
      • dist(): distance matrix

    • Package: MASS (Mondern Applied Statistics in S)
      • isoMDS(): Kruskal's non-metric MDS (an example can be found here)
      • Shepard(): for drawing Shepard diagram
      • sammon(): Sammon's non-metric MDS (similar to Kruskal's non-metric MDS but independently developed)

    • Package: smacof (Scaling by MAjorizing a COplicated Function; a paper is here)
      • smacofSym(): for symmetric dissimilarity matrices
      • smacofRect(): for rectangular input matrices, i.e., unfolding
      • smacofIndDiff(): individual difference MDS
      • smacofSphere.primal(): projection of the resulting con gurations onto spheres
      • smacofSphere.dual(): indirect function to solve linear problems, sometimes faster than primal
      • sim2diss(): convert similarity matrix to dissimilarity matrix

    • Package: labdsv (Laboratory for Dynamic Synthetic Vegephenonenology)
      • nmds(): application of isoMDS()

    • Package: vegan (R functions for vegetation ecologists)
      • metaMDS(): an integration of initMDS(), isoMDS(), postMDS(), and wascores()
      • procrustes(): for the Procrustes Problem
      • wcmdscale(): weighted classical (metric) multidimensional scaling

    • Package: rggobi
      • ggobi(): interactive multidimensional scaling using ggobi and ggvis for display

    • Useful Links

  2. SYSTAT:
    • use EM to estimate missing data in nonmetric unfolding model
    • power transformation (metric MDS)
    • log transformation (metric MDS)

  3. PERMAP: a highly entertaining, interactive tool to explore perceptual mapping

  4. SPSS: proxscal, prefscal, alscal

  5. MATLAB: mdscale()
A more complete list of MDS softwares can be found here.

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