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Classic functional diversity indices

Source: R/traits.R
trait_fd_indices.Rd

Functional richness (FRic), evenness (FEve), divergence (FDiv), dispersion (FDis) and Rao's quadratic entropy (RaoQ) for each site (Villeger et al. 2008; Laliberte and Legendre 2010), computed by FD::dbFD() and returned as a tidy table. These complement the Hill-number functional diversity of div_hill().

Usage

trait_fd_indices(
  data,
  traits,
  site = site,
  species = species,
  abundance = NULL,
  cols = tidyselect::everything(),
  dist = NULL,
  indices = c("FRic", "FEve", "FDiv", "FDis", "RaoQ"),
  m = "max"
)

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

Optional species dissimilarity (e.g. from trait_dist()); computed with Gower distance from traits if NULL.

indices

Indices to return.

m

Number of PCoA axes for FRic and FDiv: "max" or "min" (see FD::dbFD()), or a number.

Value

A tibble with the site column, nbsp (species richness), index and value.

References

Villeger, S., Mason, N. W. H. and Mouillot, D. (2008). New multidimensional functional diversity indices for a multifaceted framework in functional ecology. Ecology, 89, 2290-2301. doi:10.1890/07-1206.1

Laliberte, E. and Legendre, P. (2010). A distance-based framework for measuring functional diversity from multiple traits. Ecology, 91, 299-305. doi:10.1890/08-2244.1

Examples

aravo <- data_aravo()
trait_fd_indices(aravo$community, aravo$traits, abundance = cover,
              indices = c("FDis", "RaoQ"))
#> # A tibble: 150 x 4
#>    site   nbsp index value
#>    <chr> <int> <chr> <dbl>
#>  1 AR26     26 FDis  0.135
#>  2 AR22     28 FDis  0.136
#>  3 AR28     24 FDis  0.134
#>  4 AR01     23 FDis  0.133
#>  5 AR23     22 FDis  0.134
#>  6 AR08     28 FDis  0.136
#>  7 AR12     24 FDis  0.130
#>  8 AR61     20 FDis  0.138
#>  9 AR49     20 FDis  0.148
#> 10 AR50     21 FDis  0.146
#> # i 140 more rows