R/cop_powermds.R

In cops: Cluster Optimized Proximity Scaling

#' PCOPS version of powermds
#'
#' This is power stress with free kappa and lambda but nu is internally fixed to 1, so no weight transformation.
#' 
#' @param dis numeric matrix or dist object of a matrix of proximities
#' @param theta the theta vector of powers; a vector of length 2 where the first element is kappa (for the fitted distances), the second lambda (for the observed proximities). If a scalar is given it is recycled.  Defaults to 1,1.
#' @param type MDS type. Defaults to ratio.
#' @param ndim number of dimensions of the target space
#' @param itmaxi number of iterations. default is 10000.
#' @param weightmat (optional) a matrix of nonnegative weights
#' @param init (optional) initial configuration
#' @param stressweight weight to be used for the fit measure; defaults to 1
#' @param cordweight weight to be used for the cordillera; defaults to 0.5
#' @param q the norm of the cordillera; defaults to 1
#' @param minpts the minimum points to make up a cluster in OPTICS; defaults to ndim+1
#' @param epsilon the epsilon parameter of OPTICS, the neighbourhood that is checked; defaults to 10
#' @param rang range of the distances (min distance minus max distance). If NULL (default) the cordillera will be normed to each configuration's maximum distance, so an absolute value of goodness-of-clusteredness.
#' @param verbose numeric value hat prints information on the fitting process; >2 is extremely verbose
#' @param normed should the cordillera be normed; defaults to TRUE
#' @param scale should the configuration be scale adjusted
#' @param ... additional arguments to be passed to the fitting procedure
#'
#' @return A list with the components
#' \itemize{
#'         \item stress: the stress-1 value
#'         \item stress.m: default normalized stress
#'         \item copstress: the weighted loss value
#'         \item OC: the Optics cordillera value
#'         \item parameters: the parameters used for fitting (kappa, lambda)
#'         \item fit: the returned object of the fitting procedure
#'         \item cordillera: the cordillera object
#' }
#' @keywords multivariate
#' @import cordillera
#' @importFrom smacofx powerStressMin
cop_powermds <- function(dis,theta=c(1,1),type="ratio",weightmat=1-diag(nrow(dis)),init=NULL,ndim=2,itmaxi=10000,...,stressweight=1,cordweight=0.5,q=1,minpts=ndim+1,epsilon=10,rang=NULL,verbose=0,scale="sd",normed=TRUE) {
  if(length(theta)>3) stop("There are too many parameters in the theta argument.")
  if(length(theta)<2) theta <- rep(theta,length.out=2)
  kappa <- theta[1]
  lambda <- theta[2]
  nu <- 1
  fit <- smacofx::powerStressMin(delta=dis,type=type,kappa=kappa,lambda=lambda,nu=1,weightmat=weightmat,init=init,ndim=ndim,verbose=verbose,itmax=itmaxi,...)
   ncall <- do.call(substitute,list(fit$call,list(kappa=kappa,lambda=lambda,type=type,init=init,ndim=ndim,verbose=verbose,itmax=itmaxi)))
  fit$call <- ncall                 
  fit$kappa <- theta[1]
  fit$lambda <- theta[2]
  fit$nu <- 1
  fit$parameters <- fit$theta <- fit$pars  <- c(kappa=fit$kappa,lambda=fit$lambda)
  #fit$deltaorig <- stats::as.dist(dis)
  copobj <- copstress(fit,stressweight=stressweight,cordweight=cordweight,q=q,minpts=minpts,epsilon=epsilon,rang=rang,verbose=isTRUE(verbose>1),scale=scale,normed=normed,init=init)
  out <- list(stress=fit$stress, stress.m=fit$stress.m, copstress=copobj$copstress, OC=copobj$OC, parameters=copobj$parameters, fit=fit, copsobj=copobj)
  out 
}