bcdist {ecodist}

Bray-Curtis distance

Description

Returns the Bray-Curtis (also known as Sorenson, 1 - percent similarity) pairwise distances for the objects in the data. It is duplicated by functionality within distance but remains for backward compatibility and because it is substantially faster.

Usage

bcdist(x, rmzero = FALSE)

Arguments

x

matrix or data frame with rows as samples and columns as variables (such as species). Distances will be calculated for each pair of rows.

rmzero

If rmzero=TRUE, empty rows will be removed from the data before distances are calculated. Otherwise, the distance between two empty rows is assumed to be 0 (the default).

Value

This function returns a column-order lower-triangular distance matrix. The returned object has an attribute, Size, giving the number of objects, that is, nrow(x). The length of the vector that is returned is nrow(x)*(nrow(x)-1)/2.

Author(s)

Sarah Goslee

See Also

dist, distance

Examples

data(graze)
system.time(graze.bc <- bcdist(graze[, -c(1:2)]))
# equivalent to but much faster than:
system.time(graze.bc2 <- distance(graze[, -c(1:2)], "bray-curtis"))

all.equal(graze.bc, graze.bc2)