Pairwise associations

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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

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pairwise_association(mat, method = "condentropy")

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.

Value

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

Examples

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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)