netassoc (version 0.7.0)

pairwise_association: Pairwise associations

Description

Computes pairwise associations between every row (species) in a species x site matrix. Note that usage of this function is advantageous when non-symmetric association metrics are desired, but the pairwise computation will prevent accounting for indirect effects between species. As such this function should be considered preliminary, and its use experimental.

Usage

pairwise_association(mat, method = "condentropy")

Value

A n x n (species x species) matrix with NA diagonal values. May be non-symmetric depending on the method used.

Arguments

mat

A m x n (species x site) matrix

method

The name of a function to call to calculate an association score. Must take two vector arguments (X,Y) and return a single numeric value. Default argument uses conditional information entropy statistic, although other functions (e.g. Jaccard similarity) are possible.

Examples

nsp <- 10
nsi <- 50
m_obs <- floor(matrix(rpois(nsp*nsi,lambda=5),ncol=nsi,nrow=nsp))
m_obs[1,1:(nsi/2)] <- rpois(n=nsi/2,lambda=20)

spxsp <- pairwise_association(m_obs, method="condentropy")
image(spxsp)