hillR: hill_func_parti_pairwise – R documentation

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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,
  ...
)

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`.

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>.

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

## Not run: 
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)

## End(Not run)

hillR

Diversity Through Hill Numbers

v0.5.1

MIT + file LICENSE

Authors

Daijiang Li

Initial release

2021-03-01