Nothing
#if (!isGeneric("compress")) {
setGeneric("compress",
function (x, ...)
standardGeneric("compress"))
#}
setMethod("compress",
signature(x = "Vegsoup"),
function (x, retain) {
coverscale(x) <- "pa"
if (!missing(retain)) {
j <- match(retain, names(x))
if (any(!is.na(j))) {
x@sites <- data.frame(
compress = rep(TRUE, nrow(x)),
sites(x)[ , j[!is.na(j) ], drop = FALSE],
row.names = rownames(sites(x)))
}
else {
x@sites <- data.frame(
compress = rep(TRUE, nrow(x)),
cols = ncol(x),
row.names = rownames(sites(x)))
}
}
else {
x@sites <- data.frame(
compress = rep(TRUE, nrow(x)),
cols = ncol(sites(x)),
row.names = rownames(sites(x)))
}
x <- layers(x, collapse = "0l", aggregate = "min")
z <- taxonomy(taxonomy(x))
j <- c("abbr", "taxon", "family", "level")
j <- match(j, names(z))
z <- z[ , j[!is.na(j)] ]
x@taxonomy <- taxonomy(z)
return(x)
}
)
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