distance {ecodist}R Documentation

Calculate dissimilarity/distance metrics

Description

This function calculates a variety of dissimilarity or distance metrics. Although it duplicates the functionality of dist() and bcdist(), it is written entirely in R, and can easily be extended to include additional metrics. distance() was written for extensibility and understandability, and is not an efficient choice for use with large matrices.

Usage

distance(x, method = "euclidean")

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.
method Currently 7 dissimilarity metrics can be calculated: euclidean bray-curtis manhattan mahalanobis jaccard simple difference sorensen Partial matching will work for selecting a method.

Value

Returns a lower-triangular distance matrix as an object of class "dist".

Author(s)

Sarah Goslee <Sarah.Goslee@ars.usda.gov>

See Also

dist

Examples

data(iris)
iris.md <- distance(iris[,1:4], "mahal")

[Package ecodist version 1.2.2 Index]