#--------------------------------------------------
# Zero replacement for the logratio method
#  "martin"   : Martin-Fernandez et al.(2000, 2003)
#  "fry"      : Fry et al.(2000)
#  "aitchison": Aitchison (1986, 2003)
#
# January 23, 2006
# Developed by Hiroyoshi Arai
#--------------------------------------------------


zero.replace <- function(x, delta, total=100, method=c("martin", "fry", "aitchison")) {

	if (any(x < 0)) {
		stop("Data contains negative value(s).")
	}

	if ((delta < 0) || (total <= 0)) {
		stop("Invalid delta and/or total.")
	}

	method <- match.arg(method)
	x[is.na(x)] <- 0
	x <- x/apply(x, 1, sum)*total
	z <- apply((x == 0), 1, sum)
	d <- ncol(x)

	if ((method == "martin") && !any(z*delta >= total)) {
		x <- (1-z*delta/total)*(x != 0)*x
		x[x == 0] <- delta
	} else {
		if ((method == "fry") && !any(z*delta*(z+1)*(d-z)/d^2 >= total)) {
			x <- (1-z*delta*(z+1)*(d-z)/d^2/total)*(x != 0)*x
			x <- x+delta*(z+1)*(d-z)/d^2*(x == 0)
		} else {
			if ((method == "aitchison") && !any((x-delta*(z+1)*z/d^2*(x != 0))[x != 0] <= 0)) {
				x <- x-delta*(z+1)*z/d^2*(x != 0)
				x <- x+delta*(z+1)*(d-z)/d^2*(x == 0)
			} else {
				stop("Invalid delta.")
			}
		}
	}

	return(x)
}