cop_rstress {cops}

PCOPS version of rstress

Description

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

Usage

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

Value

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