cop_sammon function

PCOPS version of Sammon mapping from MASS

PCOPS version of Sammon mapping from MASS

Uses smacofx::sammon wrapper for MASS::sammon. The free parameter is lambda for power transformations of the observed proximities.

cop_sammon( dis, theta = 1, type = "ratio", ndim = 2, init = NULL, weightmat = NULL, itmaxi = 1000, ..., stressweight = 1, cordweight = 0.5, q = 1, minpts = ndim + 1, epsilon = 10, rang = NULL, verbose = 0, scale = "sd", normed = TRUE )

Arguments

  • dis: numeric matrix or dist object of a matrix of proximities
  • theta: the theta vector of powers; this must be a scalar of the lambda transformation for the observed proximities. Defaults to 1.
  • type: MDS type. Only "ratio" here.
  • ndim: number of dimensions of the target space
  • init: (optional) initial configuration
  • weightmat: (optional) a matrix of nonnegative weights.
  • itmaxi: number of iterations. Default is 1000.
  • ...: additional arguments to be passed to the fitting procedure
  • stressweight: weight to be used for the fit measure; defaults to 1
  • cordweight: weight to be used for the cordillera; defaults to 0.5
  • q: the norm of the corrdillera; defaults to 1
  • minpts: the minimum points to make up a cluster in OPTICS; defaults to ndim+1
  • epsilon: the epsilon parameter of OPTICS, the neighbourhood that is checked; defaults to 10
  • rang: range of the distances (min distance minus max distance). If NULL (default) the cordillera will be normed to each configuration's maximum distance, so an absolute value of goodness-of-clusteredness.
  • verbose: numeric value hat prints information on the fitting process; >2 is extremely verbose
  • scale: if TRUE the configuration is scale adjusted
  • normed: should the cordillera be normed; defaults to TRUE

Returns

A list with the components

  • stress: the stress-1
  • stress.m: default normalized stress (stress-1^2)
  • copstress: the weighted loss value
  • OC: the Optics cordillera value
  • parameters: the parameters used for fitting (lambda)
  • fit: the returned object of the fitting procedure smacofx::sammon
  • cordillera: the cordillera object