cop_sammon {cops}

PCOPS version of Sammon mapping from MASS

Description

Uses smacofx::sammon wrapper for MASS::sammon. The free parameter is lambda for power transformations of the observed proximities.

Usage

cop_sammon(
  dis,
  theta = 1,
  type = "ratio",
  ndim = 2,
  init = NULL,
  weightmat = NULL,
  itmaxi = 1000,
  ...,
  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. Defaults to 1.

type

MDS type. Only "ratio" here.

ndim

number of dimensions of the target space

init

(optional) initial configuration

weightmat

(optional) a matrix of nonnegative weights.

itmaxi

number of iterations. Default is 1000.

...

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 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

if TRUE the configuration is scale adjusted

normed

should the cordillera be normed; defaults to TRUE

Value

A list with the components

• stress: the stress-1

• stress.m: default normalized stress (stress-1^2)

• 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 smacofx::sammon

• cordillera: the cordillera object