hill_func_parti_pairwise: Pairwise comparisons for all sites.

Description

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

Usage

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

Value

a data frame with results for all pairwise comparisons.

Arguments

comm: A data frame of vegetation data. Sites as rows, species as columns.
traits: A data frame of species functional traits data. Species as rows, traits as columns. It can include both continuous and categorical data. It will be transformed into a distance matrix using `FD::gowdis(traits)`. If all traits are numeric, then it will use Euclidean distance.
traits_as_is: if FALSE (default) traits data frame will be transformed into a distance matrix. Otherwise, will use as is (i.e. traits is a symmetric distance matrix).
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.
...: additional arguments for hill_func_parti.

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>.

Chiu, Chun-Huo, and Anne Chao. Distance-Based Functional Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers. PLoS ONE 9, no. 7 (July 7, 2014): e100014. <doi:10.1371/journal.pone.0100014>.

Examples

Run this code

if (FALSE) {
dummy = FD::dummy
hill_func_parti_pairwise(comm = dummy$abun, traits = dummy$trait, q = 0)
hill_func_parti_pairwise(comm = dummy$abun, traits = dummy$trait, q = 0,
                         output = 'matrix')
hill_func_parti_pairwise(comm = dummy$abun, traits = dummy$trait, q = 0,
                         output = 'matrix', pairs = 'full')
hill_func_parti_pairwise(comm = dummy$abun, traits = dummy$trait, q = 1)
hill_func_parti_pairwise(comm = dummy$abun, traits = dummy$trait, q = 0.9999)
hill_func_parti_pairwise(comm = dummy$abun, traits = dummy$trait, q = 2)
hill_func_parti_pairwise(comm = dummy$abun, traits = dummy$trait, q = 3)
}