cop_rstress function

PCOPS version of rstress

Free parameter is kappa=2r for the fitted distances.

cop_rstress(
  dis,
  theta = 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; this must be a scalar of the kappa=2*r transformation for the fitted distances proximities. Defaults to 1. Note that what is returned is r, not kappa.
• 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. 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 stress-1 value
• stress.m: default normalized stress
• copstress: the weighted loss value
• OC: the Optics cordillera value
• parameters: the parameters used for fitting (r)
• fit: the returned object of the fitting procedure
• cordillera: the cordillera object