Nothing
setGeneric("abundant",
function (obj, threshold = 75, layers = FALSE, ...)
standardGeneric("abundant")
)
setMethod("abundant",
signature(obj = "Vegsoup"),
function (obj, threshold = 75, layers = FALSE, ...) {
if (inherits(obj, "VegsoupPartition") | inherits(obj, "VegsoupPartitionFidelity")) {
obj <- as(obj, "Vegsoup")
}
if (layers) {
r <- obj
} else {
r <- layers(obj, "0l")
}
decostand(r) <- NULL
r1 <- constancy(r)
r2 <- quantile(r, coverscale = TRUE)[ , , 3]
r3 <- quantile(r, coverscale = FALSE)[ , , 3]
r <- as.data.frame(r1)
ri <- decode(r, obj)
r$labels <- r2
r$cover <- r3
r$taxon <- ri$taxon
r$layer <- ri$layer
names(r)[ 1 ] <- "constancy"
r <- r[ r$constancy >= threshold, ]
if (layers) {
r <- r[ order(r$constancy, r$layer, r$cover, r$taxon, decreasing = TRUE), ]
} else {
r <- r[ order(r$constancy, r$cover, r$taxon, decreasing = TRUE), ]
}
return(r)
}
)
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