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### This file contains files for estimating parameters emperically.
### Estimate MU based on classified data.
estimate.MU <- function(X.spmd, CLASS.spmd, K){
p <- ncol(X.spmd)
MU.CLASS <- matrix(0, nrow = p, ncol = K)
for(i.k in 1:K){
tmp.id <- which(CLASS.spmd == i.k)
tmp.n.id <- spmd.allreduce.double(as.double(length(tmp.id)),
double(1), op = "sum")
if(length(tmp.id) > 0){
tmp.MU <- colSums(X.spmd[tmp.id,])
} else{
tmp.MU <- rep(0.0, p)
}
tmp.MU <- spmd.allreduce.double(tmp.MU, double(p), op = "sum")
MU.CLASS[, i.k] <- tmp.MU / tmp.n.id
}
MU.CLASS
} # End of estimate.MU().
### Estimate SIGMA based on classified data.
#my.estimate.sigma <- function(n, k, X.spmd, MU){
# x <- matrix(X.spmd[n,] - MU[, k], nrow = 1)
# as.vector((t(x) %*% x))
#} # End of my.estimate.sigma().
estimate.SIGMA <- function(X.spmd, MU, CLASS.spmd, K){
p <- ncol(X.spmd)
p.2 <- p * p
SIGMA.CLASS <- NULL
for(i.k in 1:K){
tmp.id <- which(CLASS.spmd == i.k)
tmp.n.id <- spmd.allreduce.double(as.double(length(tmp.id)),
double(1), op = "sum")
if(length(tmp.id) == 1){
tmp.X.spmd <- X.spmd[tmp.id,] - MU[, i.k]
dim(tmp.X.spmd) <- c(1, p)
tmp.SIGMA <- crossprod(tmp.X.spmd)
} else if(length(tmp.id) > 1){
# Version 1:
# tmp.SIGMA <- rowSums(do.call("cbind",
# lapply(tmp.id, my.estimate.sigma,
# i.k, X.spmd, MU)))
# Version 2:
# tmp.X.spmd <- t.X.spmd[tmp.id,] - MU[, i.k]
# tmp.SIGMA <- tmp.X.spmd %*% t(tmp.X.spmd)
# Version 3:
tmp.X.spmd <- W.plus.y(X.spmd[tmp.id,], -MU[, i.k],
length(tmp.id), p)
tmp.SIGMA <- crossprod(tmp.X.spmd)
} else{
tmp.SIGMA <- rep(0.0, p.2)
}
tmp.SIGMA <- spmd.allreduce.double(tmp.SIGMA, double(p.2), op = "sum")
SIGMA.CLASS[[i.k]] <- matrix(tmp.SIGMA / (tmp.n.id - 1), ncol = p)
}
SIGMA.CLASS
} # End of estimate.SIGMA().
### This function collects N.CLASS
get.N.CLASS <- function(K){
tmp.n.class <- tabulate(.pmclustEnv$CLASS.spmd, nbins = K)
spmd.allreduce.integer(as.integer(tmp.n.class), integer(K), op = "sum")
} # End of get.N.CLASS().
get.CLASS <- function(PARAM){
A <- exists("CLASS", envir = .pmclustEnv)
B <- exists("CLASS.spmd", envir = .pmclustEnv)
if(A & B){
comm.stop("CLASS and CLASS.spmd both exist in .pmclustEnv")
} else{
if(A){
ret <- spmd.allgather.integer(as.integer(.pmclustEnv$CLASS.spmd),
integer(PARAM$N))
ret <- unlist(ret)
} else if(B){
ret <- as.integer(.pmclustEnv$CLASS)
} else{
comm.stop("CLASS and CLASS.spmd do not exist in .pmclustEnv")
}
}
ret
} # End of get.CLASS().
### Copy from dmvnorm() in mvtnorm package.
#logdmvnorm <- function(x, mean, sigma){
# x <- matrix(x, nrow = 1)
# distval <- mahalanobis(x, center = mean, cov = sigma)
# logdet <- sum(log(eigen(sigma, symmetric = TRUE, only.values = TRUE)$values))
# logretval <- -(ncol(x) * log(2 * pi) + logdet + distval)/2
# logretval
#} # End of logdmvnorm()
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