Transform a distance matrix into a similarity matrix Leinster2012divent. Similarity between two species is defined either by a negative exponential function of their distance or by the complement to 1 of their normalized distance (such that the most distant species are 1 apart).

fun_similarity(distances, exponential = TRUE, rate = 1, check_arguments = TRUE)

Arguments

distances

A distance matrix or an object of class stats::dist

exponential

If TRUE, similarity is \(e^{-r \delta}\), where \(r\) is argument rate. If FALSE, it is \(1 - \delta / \max(\delta)\).

rate

The decay rate of the exponential similarity.

check_arguments

If TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

Value

A similarity matrix.

References

Examples

# Similarity between Paracou 6 species
hist(fun_similarity(paracou_6_fundist))