hill_taxa_parti_pairwise {hillR}

Pairwise comparisons for all sites

Description

Calculate pairwise taxonomic gamma, alpha, and beta diversity for communities, as well as site similarity. It is based on hill_taxa_parti. If comm has >2 sites, this function will give results for all pairwise comparisons.

Usage

hill_taxa_parti_pairwise(
  comm,
  q = 0,
  rel_then_pool = TRUE,
  output = c("data.frame", "matrix"),
  pairs = c("unique", "full"),
  .progress = TRUE,
  show_warning = TRUE,
  ...
)

Arguments

comm

A data frame of vegetation data. Sites as rows, species as columns.

q

Hill number, q = 0 (default) to get species richness, q = 1 to get shannon entropy, q = 2 will give inverse Simpson.

rel_then_pool

default is TRUE. Abundance of species are first changed to relative abundance within sites, then pooled into one assemblage. If FALSE, sites are pooled first, then change abundance of species to relative abundance.

output

output type: data.frame (default) or matrix. If matrix, then this function will return a list of matrices.

pairs

full or unique (default). Do you want to compare all possible pairs (i.e. n^2) or just unique pairs (i.e. choose(n, 2))?

.progress

Whether to show progress bar. Default is 'TRUE'.

show_warning

whether to print warning, default is TRUE.

...

other arguments in hill_taxa_parti().

Value

A data frame with results for all pairwise comparisons.

References

Chao, Anne, Chun-Huo Chiu, and Lou Jost. Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers. Annual Review of Ecology, Evolution, and Systematics 45, no. 1 (2014): 297–324. <doi:10.1146/annurev-ecolsys-120213-091540>.

Jost, Lou. Entropy and diversity. Oikos 113, no. 2 (2006): 363-375. <doi:10.1111/j.2006.0030-1299.14714.x>.

See Also

hill_taxa_parti

Examples

## Not run: 
dummy = FD::dummy
hill_taxa_parti_pairwise(comm = dummy$abun, q = 0)
hill_taxa_parti_pairwise(comm = dummy$abun, q = 0, output = 'matrix')
hill_taxa_parti_pairwise(comm = dummy$abun, q = 1)
hill_taxa_parti_pairwise(comm = dummy$abun, q = 0.9999999)
hill_taxa_parti_pairwise(comm = dummy$abun, q = 0.9999999, rel_then_pool = FALSE)
hill_taxa_parti_pairwise(comm = dummy$abun, q = 1, rel_then_pool = FALSE)
hill_taxa_parti_pairwise(comm = dummy$abun, q = 2)
hill_taxa_parti_pairwise(comm = dummy$abun, q = 3)

## End(Not run)