Bray-Curtis distance

Description

Returns the Bray-Curtis (also known as Sorenson, 1 - percent similarity) pairwise distances for the objects in the data. It has been superseded by distance() but remains for backward compatibility.

Usage

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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 rzero=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, Sarah.Goslee@ars.usda.gov

See Also

dist

Examples

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data(iris)
iris.bc <- bcdist(iris[,1:4])
# equivalent to
iris.bc2 <- distance(iris[,1:4], "bray-curtis")