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# Indicator species analysis by Murdoch preference function
# to do: documentation
setGeneric("murdoch",
function (x, ...)
standardGeneric("murdoch")
)
setMethod("murdoch",
signature(x = "VegsoupPartition"),
function (x, minplt, type, ...) {
if (getK(x) == 1)
stop("meaningless with k = ", getK(x))
if (missing(minplt))
minplt <- 1
if (missing(type))
part <- partitioning(x)
if (any(table(part) == 1)) {
stop("singleton present")
}
ks <- getK(x)
res <- matrix(0, nrow = dim(x)[2], ncol = ks)
dimnames(res) <- list(colnames(x), 1:ks)
pval <- matrix(0, nrow = dim(x)[2], ncol = ks)
dimnames(pval) <- list(colnames(x), 1:ks)
res.ls <- vector("list", length = ks)
names(res.ls) <- 1:ks
for (i in 1:ks) {
res.ls[[i]] <- optpart::murdoch(as.logical(x),
part == i, minplt = minplt)
res[,i] <- res.ls[[i]]$murdoch
pval[,i] <- round(res.ls[[i]]$pval, 3)
}
return(c(res.ls, list(murdoch = res, pval = pval)))
}
)
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