tax2dist {rdiversity}

Generate taxonomic distance matrix

Description

Calculates taxonomic distances between species.

Usage

tax2dist(lookup, tax_distance, precompute_dist = TRUE)

Arguments

lookup

data.frame with colnames corresponding to nested taxonomic levels, e.g. c('Species', 'Genus', 'Family', 'Subclass')

tax_distance

vector with the distances attributed to taxonomic levels defined in lookup. The highest distance is the distance attributed to species that are not the same at any recorded taxonomic level. e.g. c(Species = 0, Genus = 1, Family = 2, Subclass = 3, Other = 4) from Shimatani.

precompute_dist

object of class logical or numeric. When TRUE (by default) a distance matrix is generated and stored in slot distance, when FALSE no distance matrix is generated, and when numeric a distance matrix is generated until the number of species exceeds the defined value.

Value

tax2dist() returns an object of class distance containing a matrix of pairwise taxonomic distances

References

Shimatani, K. 2001. On the measurement of species diversity incorporating species differences. Oikos 93:135–147.

Examples

# 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)

# Generate pairwise distances
distance <- tax2dist(lookup, tax_distance)
similarity <- dist2sim(distance, "linear")