Nothing
# 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))
}
)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.