cop_cmdscale {cops}

PCOPS version of strain

Description

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

Usage

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

Value

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