R: R stress SMACOF

rStressMin {smacofx}

R Documentation

R stress SMACOF

Description

An implementation to minimize r-stress by majorization with ratio, interval and ordinal optimal scaling. Uses a repeat loop.

Usage

rStressMin(
  delta,
  r = 0.5,
  type = c("ratio", "interval", "ordinal"),
  ties = "primary",
  weightmat = 1 - diag(nrow(delta)),
  init = NULL,
  ndim = 2,
  acc = 1e-06,
  itmax = 10000,
  verbose = FALSE,
  principal = FALSE
)

rstressMin(
  delta,
  r = 0.5,
  type = c("ratio", "interval", "ordinal"),
  ties = "primary",
  weightmat = 1 - diag(nrow(delta)),
  init = NULL,
  ndim = 2,
  acc = 1e-06,
  itmax = 10000,
  verbose = FALSE,
  principal = FALSE
)

rstressmds(
  delta,
  r = 0.5,
  type = c("ratio", "interval", "ordinal"),
  ties = "primary",
  weightmat = 1 - diag(nrow(delta)),
  init = NULL,
  ndim = 2,
  acc = 1e-06,
  itmax = 10000,
  verbose = FALSE,
  principal = FALSE
)

rstress(
  delta,
  r = 0.5,
  type = c("ratio", "interval", "ordinal"),
  ties = "primary",
  weightmat = 1 - diag(nrow(delta)),
  init = NULL,
  ndim = 2,
  acc = 1e-06,
  itmax = 10000,
  verbose = FALSE,
  principal = FALSE
)

Arguments

`delta`	dist object or a symmetric, numeric data.frame or matrix of distances
`r`	power of the transformation of the fitted distances (corresponds to kappa/2 in power stress); defaults to 0.5 for standard stress
`type`	what type of MDS to fit. Currently one of "ratio", "interval" or "ordinal". Default is "ratio".
`ties`	the handling of ties for ordinal (nonmetric) MDS. Possible are "primary" (default), "secondary" or "tertiary".
`weightmat`	a matrix of finite weights.
`init`	starting configuration
`ndim`	dimension of the configuration; defaults to 2
`acc`	numeric accuracy of the iteration. Default is 1e-6.
`itmax`	maximum number of iterations. Default is 10000.
`verbose`	should iteration output be printed; if > 1 then yes
`principal`	If 'TRUE', principal axis transformation is applied to the final configuration

Value

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

delta: Observed, untransformed dissimilarities
tdelta: Observed explicitly transformed dissimilarities, normalized
dhat: Explicitly transformed dissimilarities (dhats), optimally scaled and normalized
confdist: Configuration dissimilarities
conf: Matrix of fitted configuration
stress: Default stress (stress 1; sqrt of explicitly normalized stress)
spp: Stress per point
ndim: Number of dimensions
model: Name of smacof model
niter: Number of iterations
nobj: Number of objects
type: Type of MDS model
weightmat: weighting matrix as supplied
stress.m: Default stress (stress-1^2)
tweightmat: transformed weighting matrix (here NULL)

Examples

dis<-smacof::kinshipdelta
res<-rStressMin(as.matrix(dis),type="ordinal",r=1,itmax=1000)
res
summary(res)
plot(res)