Nothing
# summary statistics
# Tukey Five-Number Summary
setGeneric("Fivenum",
function (obj, na.rm = TRUE, recode = FALSE)
standardGeneric("Fivenum")
)
setMethod("Fivenum",
signature(obj = "VegsoupPartition"),
function (obj, na.rm = TRUE, recode = FALSE) {
if (recode & !is.null(decostand(obj))) {
message("disregard decostand method for calculations")
decostand(obj) <- NULL
}
tmp <- as.numeric(obj)
# if (!na.rm)
#tmp[tmp == 0] <- NA
tmp <- aggregate(tmp,
by = list(partitioning(obj)),
FUN = function (x) stats::fivenum(x, na.rm = TRUE), simplify = FALSE)
part <- tmp[, 1]
tmp <- tmp[, -1]
res <- array(0, dim = c(dim(tmp)[2], dim(tmp)[1], 5),
dimnames = list(names(tmp), part,
c("min", "lower", "median", "upper", "max")))
for (i in 1:5) {
for (j in 1:nrow(res)) {
# j = 1; i = 1
res[j, , i] <- sapply(tmp[, j], function (x) x[i])
}
}
if (recode) {
for (i in 1:dim(res)[3]) {
tmp <- res[, , i]
mode(tmp) <- "numeric"
vals <- as.character(cut(tmp,
breaks = c(0, coverscale(obj)@lims),
labels = coverscale(obj)@codes,
))
tmp.i <- tmp
mode(tmp.i) <- "character"
tmp.i[] <- vals
res[, , i] <- tmp.i
}
res[is.na(res)] <- "."
}
return(invisible(res))
}
)
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