rStressMin function

R stress SMACOF

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

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

Returns

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: Transformed fitted configuration distances
• 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)

See Also

smacofSym