data(Byar)
# Transformation skewed variables
Byar$Size.of.primary.tumour <- sqrt(Byar$Size.of.primary.tumour)
Byar$Serum.prostatic.acid.phosphatase <-
log(Byar$Serum.prostatic.acid.phosphatase)
# Order variables (Continuous, ordinal, nominal)
Y <- as.matrix(Byar[, c(1, 2, 5, 6, 8, 9, 10, 11, 3, 4, 12, 7)])
# Start categorical variables at 1 rather than 0
Y[, 9:12] <- Y[, 9:12] + 1
# Standardise continuous variables
Y[, 1:8] <- scale(Y[, 1:8])
# Merge categories of EKG variable for efficiency
Yekg <- rep(NA, nrow(Y))
Yekg[Y[,12]==1] <- 1
Yekg[(Y[,12]==2)|(Y[,12]==3)|(Y[,12]==4)] <- 2
Yekg[(Y[,12]==5)|(Y[,12]==6)|(Y[,12]==7)] <- 3
Y[, 12] <- Yekg
argList <- list(X=Y, G=3, CnsIndx=8, OrdIndx=11, Nnorms=20000,
MaxIter=500, model="EVI", store.params=FALSE, scale=TRUE,
startCL="kmeans", autoStop=FALSE, ma.band=50, stop.tol=NA)
## Not run: ------------------------------------
# res <- clustMDlist(argList)
#
## ---------------------------------------------
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