R/vegdist.R

In vegsoup: Classes and Methods for Phytosociology

#	dissimilarity

#	vegan defines:
#	vegdist(x, method="bray", binary=FALSE, diag=FALSE,
#	upper=FALSE, na.rm = FALSE, ...)
#if (!isGeneric("vegdist")) {
setGeneric("vegdist",
	function (x, method = "bray", binary = FALSE, diag = FALSE,
	upper = FALSE, na.rm = FALSE, ...)
		standardGeneric("vegdist")
)
#}

#if (!isGeneric("vegdist <-")) {
setGeneric("vegdist<-",
	function (x, value)
		standardGeneric("vegdist<-")
)
#}

setMethod("vegdist",
	signature(x = "Vegsoup"),
	function (x, ...) {
		x@dist
	}
)

setReplaceMethod("vegdist",
	signature(x = "Vegsoup", value = "character"),
	function (x, value) {
		#	from vegan::vegdist
		METHODS <- c("manhattan", "euclidean", "canberra", "bray",
		"kulczynski", "gower", "morisita", "horn", "mountford",
		"jaccard", "raup", "binomial", "chao", "altGower", "cao")
		method <- METHODS[pmatch(value, METHODS)]
		
		if (is.na(method))
			stop("invalid distance method")
		if (method == -1) 
			stop("ambiguous distance method")
		x@dist <- method

		return(x)
	}
)

setReplaceMethod("vegdist",
	signature(x = "VegsoupPartition", value = "character"),
	function (x, value) {
		#	from vegan::vegdist
		METHODS <- c("manhattan", "euclidean", "canberra", "bray",
		"kulczynski", "gower", "morisita", "horn", "mountford",
		"jaccard", "raup", "binomial", "chao", "altGower", "cao")
		method <- METHODS[pmatch(value, METHODS)]
		
		if (is.na(method))
			stop("invalid distance method")
		if (method == -1)
			stop("ambiguous distance method")
		
		if (method != x@partitioning.method) {
			x@dist <- method
			#	recompute
			x <- VegsoupPartition(x, k = getK(x), method = x@partitioning.method)
			message("recomputed partitioning")
		}
		return(x)
	}
)

#	vegan defines:
#   distconnected(dis, toolong = 1, trace = TRUE)
#	connectedness of dissimilarities

#if (!isGeneric("distconnected<-")) {
setGeneric("distconnected",
	function (dis, toolong = 1, trace = TRUE)
		standardGeneric("distconnected")
)
#}

setMethod("distconnected",
	signature(dis = "Vegsoup"),
	function (dis, toolong = 1, trace = TRUE) {
		vegan::distconnected(as.dist(dis))
	}
)