stop_smddae function

STOPS version of sparsified multidimensional distance analysis for fixed eps and tau

smdda with free parameters tau and epsilon.

stop_smddae(
  dis,
  theta = c(100, 100),
  type = "ratio",
  weightmat = 1 - diag(nrow(dis)),
  init = NULL,
  ndim = 2,
  itmaxi = 10000,
  ...,
  stressweight = 1,
  structures = c("cclusteredness", "clinearity", "cdependence", "cmanifoldness",
    "cassociation", "cnonmonotonicity", "cfunctionality", "ccomplexity", "cfaithfulness",
    "cregularity", "chierarchy", "cconvexity", "cstriatedness", "coutlying",
    "cskinniness", "csparsity", "cstringiness", "cclumpiness", "cinequality"),
  strucweight = rep(1/length(structures), length(structures)),
  strucpars,
  verbose = 0,
  stoptype = c("additive", "multiplicative"),
  registry = struc_reg
)

Arguments

• dis: numeric matrix or dist object of a matrix of proximities
• theta: the theta vector of explicit parameters; first is tau for the neighboourhood, second is epsilon for isomapdist. Defaults to 100, 100.
• type: MDS type.
• weightmat: (optional) a matrix of nonnegative weights
• init: (optional) initial configuration
• ndim: number of dimensions of the target space
• itmaxi: 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: a character vector listing the structure indices to use. They always are called "cfoo" with foo being the structure.
• strucweight: weight to be used for the structures; defaults to 1/number of structures
• strucpars: a list of parameters for the structuredness indices; each list element corresponds to one index in the order of the appearance in structures
• verbose: numeric value hat prints information on the fitting process; >2 is extremely verbose
• stoptype: which weighting to be used in the multi-objective optimization? Either 'additive' (default) or 'multiplicative'.
• registry: registry object with c-structuredness indices.

Returns

A list with the components

• stress: the stress-1 value
• stress.m: default normalized stress
• stoploss: the weighted loss value
• struc: the structuredness indices
• parameters: the parameters used for fitting (tau)
• fit: the returned object of the fitting procedure
• stopobj: the stopobj object