ecol.dist {fossil}

Creating a Distance Matrix

Description

Create a distance matrix between any number of locations

Usage

ecol.dist(x, method = sorenson, type = "dis")
dino.dist(x, method = sorenson, type = "dis")

Arguments

x

matrix of taxa (or equivalent data) in rows by columns of localities (or equivalent)

method

the distance/similarity index to compute

type

if the matrix is to be a distance ('dis') or similarity ('sim) matrix

Details

This will create a distance (or similarity) matrix using any of the provided indices: sorenson, simpson, bray.curtis, jaccard, morisita.horn, chao.jaccard and chao.sorenson. Creating a distance matrix will give a value of 1 for the most distantly related sites, while similarity index will give a value of 1 for the most similar sites.

dino.dist is an old name for the function, and is in the process of being deprecated.

Value

A distance matrix (lower triangle) giving the pairwise distance indices between all points.

Note

To use a user generated distance index, type the name of the function to be used for method, and the function will use that function instead. Note that the function internally provides two equal length vectors at a time to the distance calculation function.

Author(s)

Matthew Vavrek

See Also

sorenson, simpson, bray.curtis, jaccard, morisita.horn, chao.jaccard and chao.sorenson

Examples

##example using fdata.mat
data(fdata.mat)
ecol.dist(fdata.mat)
ecol.dist(fdata.mat,simpson,"sim")