bcdist: Bray-Curtis distance

Description Usage Arguments Value Author(s) See Also Examples

View source: R/bcdist.R

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

1
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

1
2
3
4
5
6
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)

ecodist documentation built on July 13, 2017, 9:02 a.m.