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Standardised effect sizes from null models

Source: R/traits.R
trait_ses.Rd

Compares an observed functional diversity index with its distribution under a null model, to ask whether communities are more (divergence, e.g. limiting similarity) or less (convergence, e.g. environmental filtering) functionally diverse than expected by chance (de Bello et al. 2021, ch. 7). SES = (observed - mean null) / sd null.

Usage

trait_ses(
  data,
  traits,
  site = site,
  species = species,
  abundance = NULL,
  cols = tidyselect::everything(),
  dist = NULL,
  index = c("RaoQ", "FDis", "MPD"),
  null = c("traits", "richness", "swap"),
  times = 999
)

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.

index

Index to test: "RaoQ", "FDis" or "MPD" (abundance- weighted mean pairwise dissimilarity).

null

Null model, see Details.

times

Number of randomisations.

Value

A tibble with one row per site: observed, null_mean, null_sd, ses and p.value (two-sided rank-based).

Details

Null models:

  • "traits": shuffle trait values among species (keeps every site's species richness and abundances; tests trait structure).

  • "richness": shuffle abundances among species within each site (keeps richness and the abundance distribution of each site).

  • "swap": independent swap of the site x species matrix, keeping site and species totals (vegan::nullmodel(), "quasiswap_count").

Examples

aravo <- data_aravo()
set.seed(1)
trait_ses(aravo$community, aravo$traits, abundance = cover, times = 49)
#> # A tibble: 75 x 8
#>    site  index null   observed null_mean null_sd    ses p.value
#>    <chr> <chr> <chr>     <dbl>     <dbl>   <dbl>  <dbl>   <dbl>
#>  1 AR26  RaoQ  traits    0.186     0.201  0.0147 -1.00     0.4 
#>  2 AR22  RaoQ  traits    0.192     0.207  0.0134 -1.13     0.36
#>  3 AR28  RaoQ  traits    0.189     0.203  0.0170 -0.827    0.56
#>  4 AR01  RaoQ  traits    0.185     0.201  0.0147 -1.10     0.24
#>  5 AR23  RaoQ  traits    0.184     0.202  0.0189 -0.925    0.44
#>  6 AR08  RaoQ  traits    0.192     0.205  0.0129 -1.05     0.32
#>  7 AR12  RaoQ  traits    0.185     0.200  0.0133 -1.14     0.2 
#>  8 AR61  RaoQ  traits    0.190     0.205  0.0146 -1.02     0.48
#>  9 AR49  RaoQ  traits    0.207     0.202  0.0177  0.250    0.88
#> 10 AR50  RaoQ  traits    0.204     0.203  0.0166  0.111    0.92
#> # i 65 more rows