stop_cmdscale: STOPS version of strain

In stops: Structure Optimized Proximity Scaling

STOPS version of strain

Description

The free parameter is lambda for power transformations of the observed proximities.

Usage

stop_cmdscale(
  dis,
  theta = 1,
  type = "ratio",
  weightmat = NULL,
  ndim = 2,
  init = NULL,
  ...,
  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"),
  itmaxi = 1000,
  add = TRUE
)

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.
type	MDS type. Ignored here.
weightmat	(optional) a matrix of nonnegative weights. Not used.
ndim	number of dimensions of the target space
init	(optional) initial configuration
...	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
stoptype	How to construct the target function for the multi objective optimization? Either 'additive' (default) or 'multiplicative'
itmaxi	number of iterations. No effect here.
add	if TRUE dis is made to Euclidean disatnces

Value

A list with the components

• stress: the badness-of-fit value (this isn't stress here but 1-(sum_ndim(max(eigenvalues,0))/sum_n(max(eigenvalues,0)), 1-GOF[2])

• stress.m: explictly normalized stress (manually calculated)

• stoploss: the weighted loss value

• indices: the values of the structuredness indices

• parameters: the parameters used for fitting (lambda)

• fit: the returned object of the fitting procedure, which is cmdscalex object with some extra slots for the parameters and stresses

• stopobj: the stopobj object

stops documentation built on Dec. 12, 2023, 3:02 a.m.