cop_powersammon function

PCOPS version of sammon with powers

PCOPS version of sammon with powers

This is power stress with free kappa and lambda but nu is fixed to -1 and the weights are delta.

cop_powersammon( dis, theta = c(1, 1), type = "ratio", weightmat = 1 - diag(nrow(dis)), init = NULL, ndim = 2, itmaxi = 10000, ..., 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; a vector of length two where the first element is kappa (for the fitted distances), the second lambda (for the observed proximities). If a scalar is given it is recycled for the free parameters. Defaults to 1 1.
  • type: MDS type. defaults to ratio.
  • weightmat: (optional) a matrix of nonnegative weights
  • init: (optional) initial configuration
  • ndim: number of dimensions of the target space
  • itmaxi: number of iterations (of powerstress). default is 10000.
  • ...: 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 cordillera; 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: should the configuration be scale adjusted
  • normed: should the cordillera be normed; defaults to TRUE

Returns

A list with the components

  • stress: the stress1 value (sqrt(stress.m))
  • stress.m: default normalized stress
  • copstress: the weighted loss value
  • OC: the Optics cordillera value
  • parameters: the explicit parameters used for fitting (kappa, lambda)
  • fit: the returned object of the fitting procedure
  • cordillera: the cordillera object