R/pointsForDistances.R

In Mthrun/Distances: Functions For Different Distance Measures

pointsForDistances <- function(distances, dim = 0 , searchMethod = "mds", plotIt = FALSE) {

#require("MASS")
#library("dbt.Plot")
distDim <- ncol(as.matrix(distances))

if (dim < 1) {
dim <- max(2, min(500, (distDim -1)))
}

if (searchMethod =="sammon") {
requireNamespace('MASS')
points <- MASS::sammon(distances, k = dim)[[1]]
}
else {
points <- cmdscale(distances, k = dim)
}

pointsDistances <- dist(points, method = "euclidean")
error <- distances - pointsDistances
MSSE <- sqrt( sum(error^2 )) / distDim
if(plotIt){
  plot(distances,pointsDistances,pch=15,col="blue",
        main=paste("Sheppard diagram, point dimension =",dim,", MSSError=",MSSE,sep=""),
        xlab="Distances",ylab="distances between points, red = identity")
  lines(pointsDistances,pointsDistances,col="red")  
  grid(max(axTicks(1))/.1,max(axTicks(2))/.1,col="black",lty="dashed")
}
return(list(points = points, MSSE = MSSE, error = error))
}