R: Power stress minimization by NEWUOA (nloptr)

powerStressFast {smacofx}

R Documentation

Power stress minimization by NEWUOA (nloptr)

Description

An implementation to minimize power stress by a derivative-free trust region optimization algorithm (NEWUOA). Much faster than majorizing as used in powerStressMin but perhaps less accurate.

Usage

powerStressFast(
  delta,
  kappa = 1,
  lambda = 1,
  nu = 1,
  weightmat = 1 - diag(nrow(delta)),
  init = NULL,
  ndim = 2,
  acc = 1e-06,
  itmax = 10000,
  verbose = FALSE
)

Arguments

`delta`	dist object or a symmetric, numeric data.frame or matrix of distances
`kappa`	power of the transformation of the fitted distances; defaults to 1
`lambda`	the power of the transformation of the proximities; defaults to 1
`nu`	the power of the transformation for weightmat; defaults to 1
`weightmat`	a matrix of finite weights
`init`	starting configuration
`ndim`	dimension of the configuration; defaults to 2
`acc`	The smallest value of the trust region radius that is allowed. If not defined, then 1e-6 will be used.
`itmax`	maximum number of iterations. Default is 10000.
`verbose`	should iteration output be printed; if > 1 then yes

Value

a 'smacofP' object (inheriting from 'smacofB', see smacofSym). It is a list with the components

delta: Observed dissimilarities, not normalized
obsdiss: Observed dissimilarities, normalized
confdist: Configuration dissimilarities, NOT normalized
conf: Matrix of fitted configuration, NOT normalized
stress: Default stress (stress 1, square root of the explicitly normalized stress on the normalized, transformed dissimilarities)
spp: Stress per point (based on stress.en)
ndim: Number of dimensions
model: Name of smacof model
niter: Number of iterations
nobj: Number of objects
type: Type of MDS model

and some additional components

gamma: Empty
stress.m: default stress for the COPS and STOP. Defaults to the explicitly normalized stress on the normalized, transformed dissimilarities
stress.en: explicitly stress on the normalized, transformed dissimilarities and normalized transformed distances
deltaorig: observed, untransformed dissimilarities
weightmat: weighting matrix

Examples

dis<-smacof::kinshipdelta
res<-powerStressFast(as.matrix(dis),kappa=2,lambda=1.5)
res
summary(res)
plot(res)