rdiversity (version 1.2.1)

similarity_shimatani: Taxonomic similarity matrix

Description

Calculates taxonomic similarity based on Shimatani's index of taxonomic similarity (see Details).

Usage

similarity_shimatani(data, lookup)

Arguments

data

\(S * N\) matrix; population counts

lookup

data.frame with colnames = c('Species', 'Genus', 'Family', 'Subclass')

Value

Returns an \(S * S\) matrix; pair-wise taxonomic similarity

Details

Shimatani's taxonomic similarity index is defined:

species.similarity	1
genus.similarity	0.75
family.similarity	0.5
subclass.similarity	0.25
other.similarity	0

References

Shimatani, K. 2001. On the measurement of species diversity incorporating species differences. Oikos 93:135<U+2013>147.

Examples

# NOT RUN {
pop <- sample(1:50, 4)
lookup <- data.frame(Subclass=c("Sapindales", "Malvales", "Fabales", 
                                  "Fabales"),      
                     Family=c("Burseraceae", "Bombacaceae", "Fabaceae", 
                              "Fabaceae"), 
                     Genus=c("Protium", "Quararibea", "Swartzia", 
                             "Swartzia"),       
                     Species= c("tenuifolium", "asterolepis",
                                    "simplex var.grandiflora",
                                    "simplex var.ochnacea"))
similarity <- similarity_shimatani(pop, lookup)

# }