Partition beta diversity into turnover and nestedness

beta_pair() computes pairwise dissimilarity between sites and splits it into turnover (species replacement) and nestedness (species loss) components following Baselga (2010, 2012). beta_multi() computes the multiple-site version for all sites in each group. Both use presence and absence, so any positive abundance counts as presence.

With index = "sorensen" the components are Simpson turnover, the nestedness-resultant component and Sorensen dissimilarity. With index = "jaccard" they are the Jaccard equivalents. With index = "bray" abundances are used: turnover is the balanced variation in abundance and nestedness the abundance gradient component of Bray-Curtis dissimilarity (Baselga 2013), matching betapart::beta.pair.abund() and betapart::beta.multi.abund().

Usage

beta_pair(
  data,
  site = site,
  species = species,
  abundance = NULL,
  index = c("sorensen", "jaccard", "bray"),
  .by = NULL
)

beta_multi(
  data,
  site = site,
  species = species,
  abundance = NULL,
  index = c("sorensen", "jaccard", "bray"),
  .by = NULL
)

Arguments

data

A data frame in long format, with one row per record.

site, species

<tidy-select> The column holding site identifiers and the column holding species names.

abundance

<tidy-select> The column holding counts. If NULL (the default), a column called abundance is used when present, otherwise every row counts as one individual.

index

Family of dissimilarity: "sorensen" or "jaccard" (presence and absence) or "bray" (abundance-based Bray-Curtis).

.by

<tidy-select> Optional grouping columns, kept in the output. Grouped data frames are also respected.

Value

beta_pair() returns a tibble with the grouping columns, site_1, site_2, turnover, nestedness and total. beta_multi() returns one row per group with n_sites, turnover, nestedness and total.

References

Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, 134-143. doi:10.1111/j.1466-8238.2009.00490.x

Baselga, A. (2012). The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Global Ecology and Biogeography, 21, 1223-1232. doi:10.1111/j.1466-8238.2011.00756.x

Baselga, A. (2013). Separating the two components of abundance-based dissimilarity: balanced changes in abundance vs. abundance gradients. Methods in Ecology and Evolution, 4, 552-557. doi:10.1111/2041-210X.12029

Examples

beta_pair(png_ants, .by = season)
#> # A tibble: 20 x 6
#>    season site_1 site_2 turnover nestedness total
#>    <chr>  <chr>  <chr>     <dbl>      <dbl> <dbl>
#>  1 dry    MW0200 MW0700    0.667    0.0108  0.677
#>  2 dry    MW0200 MW1200    0.769    0.0239  0.793
#>  3 dry    MW0200 MW1700    0.8      0.105   0.905
#>  4 dry    MW0200 MW2200    1        0       1    
#>  5 dry    MW0700 MW1200    0.615    0.0275  0.643
#>  6 dry    MW0700 MW1700    0.8      0.1     0.9  
#>  7 dry    MW0700 MW2200    0.833    0.0714  0.905
#>  8 dry    MW1200 MW1700    1        0       1    
#>  9 dry    MW1200 MW2200    0.833    0.0614  0.895
#> 10 dry    MW1700 MW2200    1        0       1    
#> 11 wet    MW0200 MW0700    0.619    0.0544  0.673
#> 12 wet    MW0200 MW1200    0.8      0.00488 0.805
#> 13 wet    MW0200 MW1700    0.9      0.0355  0.935
#> 14 wet    MW0200 MW2200    1        0       1    
#> 15 wet    MW0700 MW1200    0.55     0.075   0.625
#> 16 wet    MW0700 MW1700    0.9      0.0474  0.947
#> 17 wet    MW0700 MW2200    1        0       1    
#> 18 wet    MW1200 MW1700    0.6      0.133   0.733
#> 19 wet    MW1200 MW2200    1        0       1    
#> 20 wet    MW1700 MW2200    0.8      0.0667  0.867

beta_multi(png_ants, .by = season, index = "jaccard")
#> # A tibble: 2 x 5
#>   season n_sites turnover nestedness total
#>   <chr>    <int>    <dbl>      <dbl> <dbl>
#> 1 dry          5    0.905     0.0296 0.935
#> 2 wet          5    0.883     0.0442 0.927