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snow版的kmeans算法R语言实现
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# snow version of k-means clustering problem
library(snow)
# returns distances from x to each vector in y;
# here x is a single vector and y is a bunch of them;
# define distance between 2 points to be the sum of the absolute values
# of their componentwise differences; e.g., distance between (5,4.2) and
# (3,5.6) is 2+1.4=3.4
# compute distance between 2 vectors
dst <- function(x,y) {
tmpmat <- matrix(abs(x-y),byrow=T,ncol=length(x)) # note recycling
rowSums(tmpmat) # sum per row
}
# will check this worker's mchunk matrix against currctrs, the current
# centers of the groups, returning a matrix; row j of the matrix will
# consist of the vector sum of the points in mchunk closest to jth
# current center, and the count of such points
findnewgrps <- function(currctrs) {
ngrps <- nrow(currctrs)
spacedim <- ncol(currctrs) # what dimension space are we in?
# set up the return matrix
sumcounts <- matrix(rep(0,ngrps*(spacedim+1)),nrow=ngrps)
for (i in 1:nrow(mchunk)) {
dsts <- dst(mchunk[i,],t(currctrs))
j <- which.min(dsts)
sumcounts[j,] <- sumcounts[j,] + c(mchunk[i,],1)
}
sumcounts
}
# cluster kmeans execution
parkm <- function(cls,m,niters,initcenters) {
n <- nrow(m)
spacedim <- ncol(m) # what dimension space are we in?
# determine which worker gets which chunk of rows of m
options(warn=-1)
# If warn is negative all warnings are ignored
ichunks <- split(1:n,1:length(cls)) # cycling split n into cls groups
options(warn=0)
# If warn is zero (the default) warnings are stored until the top–level function returns.
# form row chunks
mchunks <- lapply(ichunks,function(ichunk) m[ichunk,])
# return row data m[ichunk,]
mcf <- function(mchunk) mchunk <<- mchunk
# To force variable mchunk global using assignment '<<-'.
# send row chunks to workers; each chunk will be a global variable at
# the worker, named mchunk
# clusterApply cycling apply mcf on mchunks to snow cluster(cls)
invisible(clusterApply(cls,mchunks,mcf)) # invisible: do not print when they are not assigned.
# send dst() to workers
clusterExport(cls,"dst") # assign global values on master to each node
# start iterations
centers <- initcenters
for (i in 1:niters) {
sumcounts <- clusterCall(cls,findnewgrps,centers)
# each node call findnewgrps, with centers sent to each node
tmp <- Reduce("+",sumcounts)
centers <- tmp[,1:spacedim] / tmp[,spacedim+1]
# if a group is empty, let's set its center to 0s
centers[is.nan(centers)] <- 0
}
centers
}
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