hill_func_parti: Decompostion of functional diversity through Hill Numbers

Description

Calculate functional gamma, alpha, and beta diversity for all communities, as well as site similarity. These values are based on ALL communities.

Usage

hill_func_parti(
  comm,
  traits,
  traits_as_is = FALSE,
  q = 0,
  base = exp(1),
  check_data = TRUE,
  rel_then_pool = TRUE,
  ord = c("podani", "metric"),
  stand_dij = FALSE,
  show_warning = TRUE
)

Value

a data frame with one row (across all sites), including these columns: q, RaoQ of pooled assemblage, gamma diversity, alpha diversity, beta diversity, local species overlap (similar to Sorensen), and region species overlap (similar to Jaccard). See Chiu and Chao 2014 Table 3 for more information.

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.
base: default is exp(1), the base of log.
check_data: whether to check data first? Default is TRUE.
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.
ord: ord in FD::gowdis.
stand_dij: whether to standardize distance matrix to have max value of 1? Default is FALSE.
show_warning: whether to print warning, default is TRUE.

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

dummy = FD::dummy
hill_func_parti(comm = dummy$abun, traits = dummy$trait, q = 0)
hill_func_parti(comm = dummy$abun, traits = dummy$trait, q = 1)
hill_func_parti(comm = dummy$abun, traits = dummy$trait, q = 0.9999)
hill_func_parti(comm = dummy$abun, traits = dummy$trait, q = 2)
hill_func_parti(comm = dummy$abun, traits = dummy$trait, q = 3)