cop_sammon: PCOPS version of Sammon mapping from MASS

In cops: Cluster Optimized Proximity Scaling

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

cops documentation built on Feb. 2, 2024, 3:02 p.m.