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## gradientDist - function for finding distance along gradient
## given object (a vector or something coercible to) that
## represents the gradient position, standardise to locations
## into the range 0, ..., 1
gradientDist <- function(object, ...) {
UseMethod("gradientDist")
}
gradientDist.default <- function(object, na.rm = TRUE, ...) {
object <- as.vector(object)
minD <- min(object, na.rm = na.rm)
k <- if(any(object < 0, na.rm = na.rm)) {
minD
} else {
.Machine$double.eps
}
ran <- max(object, na.rm = na.rm)
ran <- ran - minD
ran <- pmax(k, ran, na.rm = na.rm)
object <- object - minD
object <- object / ran
class(object) <- "gradientDist"
object
}
gradientDist.cca <- function(object, na.rm = TRUE, axis = 1L,
scaling = 0, ...) {
if(length(axis) > 1L) {
axis <- axis[1L]
warning("Only the first element of `axis` used.")
}
scrs <- as.vector(scores(object, choices = axis, scaling = scaling,
display = "sites", ...))
gradientDist.default(scrs, na.rm = na.rm, ...)
}
gradientDist.prcurve <- function(object, na.rm = TRUE, ...) {
scrs <- scores(object)
gradientDist.default(scrs, na.rm = na.rm, ...)
}
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