cop_cmdscale function

PCOPS version of strain

The free parameter that pcops optimizes over is lambda for power transformations of the observed proximities.

cop_cmdscale(
  dis,
  theta = 1,
  type = "ratio",
  weightmat = NULL,
  ndim = 2,
  init = NULL,
  itmaxi = 1000,
  add,
  ...,
  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.
• type: MDS type. Ignored here.
• weightmat: (optional) a matrix of nonnegative weights
• ndim: number of dimensions of the target space
• init: (optional) initial configuration
• itmaxi: number of iterations. No effect here.
• add: should the dissimilarities be made Euclidean? Defaults to TRUE.
• ...: additional arguments to be passed to the fitting procedure smacofx::cmdscale. Note we always use eig=TRUE and that can't be changed (we need the GOF). Also default if nothing is supplied is to use add=TRUE which in my opinion one always should to avoid negative eigenvalues.
• 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: should the configuration be scale adjusted
• normed: should the cordillera be normed; defaults to TRUE

Returns

A list with the components

• stress: the badness-of-fit value (this isn't stress here but 1-(sum_ndim(max(eigenvalues,0))/sum_n(max(eigenvalues,0)), 1-GOF[2])
• stress.m: default normalized stress (manually calculated)
• 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, which is cmdscalex object with some extra slots for the parameters and stresses
• cordillera: the cordillera object