rdiversity (version 2.0)

taxvec: taxvec

Description

Calculate the taxonomic similarity of a single species to all other species. Used by metacommunity() to generate a similarity matrix line-by-line when one was not precalculated by tax2dist().

Usage

taxvec(similarity, row)

Arguments

similarity

An object of class similarity (not containing a similarity matrix).

row

integer denoting which row of the similarity matrix is to be calculated.

Examples

# NOT RUN {
# Create Lookup table
Species <- c("tenuifolium", "asterolepis", "simplex var.grandiflora", "simplex var.ochnacea")
Genus <- c("Protium", "Quararibea", "Swartzia", "Swartzia")
Family <- c("Burseraceae", "Bombacaceae", "Fabaceae", "Fabaceae")
Subclass <- c("Sapindales", "Malvales", "Fabales", "Fabales")
lookup <- cbind.data.frame(Species, Genus, Family, Subclass)

# Assign values for each level (Shimatani's taxonomic distance)
tax_distance <- c(Species = 0, Genus = 1, Family = 2, Subclass = 3, Other = 4)

dist <- tax2dist(lookup, tax_distance, precompute_dist = FALSE)
similarity <- dist2sim(dist, "linear")
taxvec(similarity, 1)
# }
# NOT RUN {
# }