Pairwise dissimilarity as a distance matrix

Returns one component of beta_pair(), or one dissimilarity of beta_hill_pair(), as a stats::dist object, ready for ordination and testing with vegan, for example vegan::metaMDS(), vegan::adonis2() or vegan::betadisper(), or for clustering with stats::hclust().

Usage

beta_dist(x, component = NULL, q = NULL)

Arguments

x

A td_beta_pair tibble from beta_pair() or a td_beta_hill_pair tibble from beta_hill_pair(), without groups.

component

For beta_pair() output: "total", "turnover" or "nestedness" (default "total"). For beta_hill_pair() output: one of its dis_ columns (default "dis_sorensen").

q

For beta_hill_pair() output with several orders, the order to use.

Value

A dist object labelled with the site names, in their order of first appearance.

Examples

d <- beta_dist(beta_pair(png_ants[png_ants$season == "wet", ]))
hclust(d)
#> 
#> Call:
#> hclust(d = d)
#> 
#> Cluster method   : complete 
#> Number of objects: 5 
#> 

wet <- png_ants[png_ants$season == "wet", ]
beta_dist(beta_hill_pair(wet, abundance = workers), q = 2)
#>           MW0200    MW0700    MW1200    MW1700
#> MW0700 0.8931865                              
#> MW1200 0.8934988 0.5378074                    
#> MW1700 0.9999783 0.9999473 0.9493274          
#> MW2200 1.0000000 1.0000000 1.0000000 0.9811531