fill: Matrix fill of species matrix

In vegsoup: Classes and Methods for Phytosociology

Description

Calculates the proportion (percentage) of all non zero elements in a species matrix.

Usage

  fill(obj)

Arguments

obj	Vegsoup* object.

Value

returns a vector of length one and mode "numeric"

Author(s)

Roland Kaiser

See Also

nestedtemp in vegan for nestedness indices.

Examples

require(vegsoup)

data(barmstein)

fill(barmstein)

# relation of matrix fill and number of occurences
data(windsfeld)

# unify layer and transform to presence/absence
x <- compress(windsfeld)

# number of occurences
jj <- colSums(x)
i <- sort(unique(jj))

# compute matrix fill for each occurence treshold
r <- t(sapply(i, function (y) {
	xi <- x[ , match(names(jj[ jj >= y ]), colnames(x)) ]
	c(dim(xi), fill(xi))
}))

par(mfrow = c(2,2))
plot(i, r[, 1], type = "b",
	xlab = "occurence threshold", ylab = "number of sites")

plot(i, r[, 2], type = "b",
	xlab = "occurence threshold", ylab = "number of species")

plot(i, r[, 1] / r[, 2], type = "b",
	xlab = "occurence threshold", ylab = "number of sites / number of species")
	
plot(i, r[, 3], type = "b",
	xlab = "occurence threshold", ylab = "matrix fill")
dev.off()

vegsoup documentation built on Feb. 24, 2021, 3 a.m.