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)
A distance matrix or an object of class stats::dist
If TRUE
, similarity is \(e^{-r \delta}\),
where \(r\) is argument rate
.
If FALSE
, it is \(1 - \delta / \max(\delta)\).
The decay rate of the exponential similarity.
If TRUE
, the function arguments are verified.
Should be set to FALSE
to save time when the arguments have been checked elsewhere.
A similarity matrix.
# Similarity between Paracou 6 species
hist(fun_similarity(paracou_6_fundist))