packrat/lib-R/x86_64-w64-mingw32/3.6.1/cluster/tests/clara-ex.R

In jmcascalheira/LGMIberiaCluster: Research compendium for the paper "Human adaptations and palaeoenvironmental record during the Last Glacial Maximum in the Iberian Peninsula"

#### These are *NOT* compared with output in the released version of
###  'cluster'  currently

library(cluster)

source(system.file("test-tools.R", package = "cluster"), keep.source = FALSE)
## -> showProc.time() ...  & doExtras

data(xclara)
## Try 100 times *different* random samples -- for reliability:
nSim <- 100
nCl <- 3 # = no.classes
showProc.time()

## unknown problem: this is still platform dependent to some extent:
set.seed(107)# << reproducibility; somewhat favorable with "small iDoubt"
cl <- replicate(nSim, clara(xclara, nCl, rngR = TRUE)$cluster)
tcl <- apply(cl,1, tabulate, nbins = nCl)
showProc.time()
## those that are not always in same cluster (5 out of 3000 for this seed):
(iDoubt <- which(apply(tcl,2, function(n) all(n < nSim))))

if(doExtras) {
    if(getRversion() < "3.2.1")
	lengths <- function (x, use.names = TRUE) vapply(x, length, 1L, USE.NAMES = use.names)
    rrr <- lapply(1:128, function(iseed) {
        set.seed(iseed)
	cat(iseed, if(iseed %% 10 == 0) "\n" else "")
        cl <- replicate(nSim, clara(xclara, nCl, rngR = TRUE)$cluster)
        tcl <- apply(cl,1, tabulate, nbins = nCl)
        which(apply(tcl,2, function(n) all(n < nSim)))
    }); cat("\n")
    showProc.time()
    cat("Number of cases which \"changed\" clusters:\n")
    print(lengths(rrr))
    ## compare with "true" -- are the "changers" only those with small sil.width?
    ## __TODO!__
    showSys.time(px <- pam(xclara,3))# 1.84 on lynne(2013)

} ## doExtras


if(length(iDoubt)) { # (not for all seeds)
  tabD <- tcl[,iDoubt, drop=FALSE]
  dimnames(tabD) <- list(cluster = paste(1:nCl), obs = format(iDoubt))
  print( t(tabD) ) # how many times in which clusters
}