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Rao's quadratic entropy: alpha, beta and gamma functional diversity

Source: R/traits.R
trait_rao.Rd

Partitions functional diversity across sites with Rao's quadratic entropy, using the equivalent-numbers correction of de Bello et al. (2010) so that beta = gamma / alpha and is not underestimated. Sites are weighted equally. Dissimilarities are scaled to a maximum of 1.

Usage

trait_rao(
  data,
  traits = NULL,
  site = site,
  species = species,
  abundance = NULL,
  cols = tidyselect::everything(),
  dist = NULL
)

Arguments

data

A data frame in long format, with one row per record.

traits

A data frame of traits, one row per species, with a column whose name matches the species column of data.

site, species

<tidy-select> The column holding site identifiers and the column holding species names.

abundance

<tidy-select> The column holding counts. If NULL (the default), a column called abundance is used when present, otherwise every row counts as one individual.

cols

<tidy-select> Trait columns of traits.

dist

Species dissimilarity; computed with Gower distance from traits if NULL. Use a dissimilarity of 1 between all species for taxonomic (Simpson) diversity.

Value

A tibble with component ("alpha", "beta", "gamma"), rao (Rao's Q, for alpha and gamma) and equivalent (equivalent numbers, 1 / (1 - Q)), plus beta_prop, the proportional turnover 1 - alpha / gamma (in equivalent numbers).

References

de Bello, F. et al. (2010). The partitioning of diversity: showing Theseus a way out of the labyrinth. Journal of Vegetation Science, 21, 992-1000. doi:10.1111/j.1654-1103.2010.01195.x

Examples

aravo <- data_aravo()
trait_rao(aravo$community, aravo$traits, abundance = cover)
#> # A tibble: 3 x 4
#>   component    rao equivalent beta_prop
#>   <chr>      <dbl>      <dbl>     <dbl>
#> 1 alpha      0.303       1.44   NA     
#> 2 beta      NA           1.08    0.0725
#> 3 gamma      0.354       1.55   NA