View source: R/pairwise_association.R
pairwise_association | R Documentation |
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.
pairwise_association(mat, method = "condentropy")
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. |
A n x n (species x species) matrix with NA diagonal values. May be non-symmetric depending on the method used.
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)
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