R: Bray-Curtis distance

bcdist {ecodist} | R Documentation

## 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)

[Package ecodist version 2.0.7 Index]