fun_similarity {divent} | R Documentation |
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).
fun_similarity(distances, exponential = TRUE, rate = 1, check_arguments = TRUE)
distances |
A distance matrix or an object of class stats::dist |
exponential |
If |
rate |
The decay rate of the exponential similarity. |
check_arguments |
If |
A similarity matrix.
Leinster T, Cobbold C (2012). “Measuring Diversity: The Importance of Species Similarity.” Ecology, 93(3), 477–489. doi:10.1890/10-2402.1.
# Similarity between Paracou 6 species
hist(fun_similarity(paracou_6_fundist))