R/order.R

In kardinal-eros/synoptic: Synoptic Tables for Vegsoup Objects

###	section of ordering functions
#	order by frequency
fq.up <- function (x) {
	r <- x[ order(-fq(x)) ]	
	return(r)
}
#	order by layer
ll.up <- function (x) {
	r <- x[ order(ll.o(x)) ]
	return(r)
}
#	order by fidelity values
fm.up <- function (x) {
	if (inherits(x, "monoptic")) {
		r <- x[ order(-c(fm(x))) ]
	} else {
		if (any(d(x))) {
			r <- x[ order(fm.m(x)) ]
		} else {
			message("no faithful species within treshold")
			r <- x
		}
	}
	
	return(r)
}
#	move sig. fisher test to table top
ft.up <- function (x, warn = TRUE) {
	if (inherits(x, "monoptic")) {
		stop("non method for class monoptic")
	} else {
		if (ft.any(x)) {
			r1 <- x[ ft.t(x) ]
			r0 <- x[ !ft.t(x) ] # do nothing
			ncc.r1 <- ft.c(r1)[ ft.t(r1) ] # ft.c is NA if not within p.max
			ncc.r1 <- sapply(ncc.r1, paste, collapse = "+")
			r1 <- r1[ order(ncc.r1) ]
			r <- c(r1, r0)
		} else {
			if (warn)
				message("not a single species is significant for a fisher test")
			r <- x
		}
	}
	
	return(r)
}
#	order by maximum cluster fidelity and decreasing frequency
fm.fq <- function (x) x[ order(fm.m(x), -fq(x)) ]
#	order by maximum cluster fidelity, layer and decreasing frequency
fm.ll.fq <- function (x) x[ order(fm.m(x), ll.o(x), -fq(x)) ]