unifrac_components: Nestedness and turnover components of unweighted UniFrac...

Description Usage Arguments Details Value References Examples

Description

Nestedness and turnover components of unweighted UniFrac distance

Usage

1
2
3
4
5
6
7
unweighted_unifrac_turnover(x, y, tree, xy_labels = NULL)

unweighted_unifrac_nestedness(x, y, tree, xy_labels = NULL)

phylosor_turnover(x, y, tree, xy_labels = NULL)

phylosor_nestedness(x, y, tree, xy_labels = NULL)

Arguments

x, y

Numeric vectors of species counts or proportions.

tree

A phylogenetic tree object.

xy_labels

A character vector of species labels for x and y.

Details

Leprieur et al. (2012) showed that measures of phylogenetic beta diversity could be partitioned into nestedness and turnover components, following the approach of Baselga (2010) for Sorenson dissimilarity.

Value

The nestedness or turnover component of the UniFrac distance between communities x and y. This quantity is undefined when either x or y have all elements equal to zero, in which case we return NaN.

References

Baselga A. Partitioning the turnover and nestedness components of beta diversity. Global Ecol. Biogeogr. 2010;19:134-143.

Leprieur F, Albouy C, De Bortoli J, Cowman PF, Bellwood DR, Mouillot D. Quantifying phylogenetic beta diversity: distinguishing between "true" turnover of lineages and phylogenetic diversity gradients. PLoS One. 2012;7(8):e42760. 10.1371/journal.pone.0042760

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
# Vectors x and y have turnover but no nestedness
x <- c(1, 1, 1, 0, 0, 0, 0, 0)
y <- c(0, 1, 1, 1, 0, 0, 0, 0)

unweighted_unifrac(x, y, leprieur_tree)
unweighted_unifrac_turnover(x, y, leprieur_tree)
unweighted_unifrac_nestedness(x, y, leprieur_tree)

phylosor(x, y, leprieur_tree)
phylosor_turnover(x, y, leprieur_tree)
phylosor_nestedness(x, y, leprieur_tree)

# Vectors y and z have nestedness but no turnover
z <- c(0, 1, 1, 1, 1, 1, 1, 1)

unweighted_unifrac(y, z, leprieur_tree)
unweighted_unifrac_turnover(y, z, leprieur_tree)
unweighted_unifrac_nestedness(y, z, leprieur_tree)

phylosor(y, z, leprieur_tree)
phylosor_turnover(y, z, leprieur_tree)
phylosor_nestedness(y, z, leprieur_tree)

kylebittinger/abdiv documentation built on Jan. 31, 2020, 3:13 p.m.