stop_sammon {stops}

STOPS version of Sammon mapping

Description

Uses MASS::sammon. The free parameter is lambda for power transformations of the observed proximities. The fitted distances power is internally fixed to 1 and the power for the weights=delta is -1.

Usage

stop_sammon(
  dis,
  theta = 1,
  ndim = 2,
  init = NULL,
  weightmat = NULL,
  itmax = 1000,
  ...,
  stressweight = 1,
  structures = c("cclusteredness", "clinearity", "cdependence", "cmanifoldness",
    "cassociation", "cnonmonotonicity", "cfunctionality", "ccomplexity", "cfaithfulness",
    "chierarchy", "cconvexity", "cstriatedness", "coutlying", "cskinniness", "csparsity",
    "cstringiness", "cclumpiness", "cinequality"),
  strucweight = rep(1/length(structures), length(structures)),
  strucpars,
  verbose = 0,
  type = c("additive", "multiplicative")
)

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.

ndim

number of dimensions of the target space

init

(optional) initial configuration

weightmat

a matrix of nonnegative weights. Has no effect here.

itmax

number of iterations

...

additional arguments to be passed to the fitting procedure

stressweight

weight to be used for the fit measure; defaults to 1

structures

which structuredness indices to be included in the loss

strucweight

weight to be used for the structuredness indices; ; defaults to 1/#number of structures

strucpars

the parameters for the structuredness indices

verbose

numeric value hat prints information on the fitting process; >2 is extremely verbose

type

How to construct the target function for the multi objective optimization? Either 'additive' (default) or 'multiplicative'

Value

A list with the components

• stress: the stress

• stress.m: default normalized stress

• stoploss: the weighted loss value

• indices: the values of the structuredness indices

• parameters: the parameters used for fitting

• fit: the returned object of the fitting procedure

• stopobj: the stopobj object