unifrac: UniFrac distance

In phyloregion: Biogeographic Regionalization and Macroecology

UniFrac distance

Description

unifrac calculates the unweighted UniFrac distance between communities.

Usage

unifrac(x, phy)

Arguments

x	a community matrix, i.e. an object of class matrix or Matrix, or an object of class phyloseq.
phy	a phylogenetic tree (object of class phylo).

Value

a dist object.

References

Lozupone C, Knight R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 71 (12):8228–35. BMC Bioinformatics 7:371.

See Also

PD, phylobeta

Examples

tree <- ape::read.tree(text ="((t1:1,t2:1)N2:1,(t3:1,t4:1)N3:1)N1;")
com <- Matrix::sparseMatrix(c(1,3,4,1,4,5,1,2,3,4,5,6,3,4,6),
  c(1,1,1,2,2,2,3,3,3,3,3,3,4,4,4),x=1,
  dimnames = list(paste0("g", 1:6), tree$tip.label))

unifrac(com, tree)

phyloregion documentation built on Aug. 15, 2023, 9:07 a.m.