fun_similarity {divent}R Documentation

Functional similarity

Description

Transform a distance matrix into a similarity matrix (Leinster and Cobbold 2012). 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).

Usage

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

Leinster T, Cobbold C (2012). “Measuring Diversity: The Importance of Species Similarity.” Ecology, 93(3), 477–489. doi:10.1890/10-2402.1.

Examples

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


[Package divent version 0.4-4 Index]