hill_func_parti_pairwise {hillR}

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>.

See Also

hill_func_parti

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)