Indicator species analysis — beta_indicator • tidydiversity

Finds species associated with groups of sites (Dufrene and Legendre 1997; De Caceres et al. 2010) using indicspecies::multipatt(), and returns a tidy table.

Usage

beta_indicator(
  data,
  site = site,
  species = species,
  abundance = NULL,
  group,
  env = NULL,
  func = c("IndVal.g", "IndVal", "r.g", "r"),
  combinations = FALSE,
  adjust = "holm",
  alpha = 0.05,
  permutations = 999
)

Arguments

data: A data frame in long format, with one row per record.
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.
group: Site variable (unquoted) defining the groups.
env: A data frame of site variables with a column named like the site column. By default, site variables are taken from data: every column that is constant within each site.
func: "IndVal.g" (group-equalised indicator value, the default), "IndVal", "r.g" or "r" (point-biserial correlation).
combinations: Allow species to indicate combinations of groups?
adjust: Correction for testing many species at once, passed to stats::p.adjust(): "holm" (the default, controls the family-wise error rate), "fdr" (false discovery rate) or "none".
alpha: Return only species with adjusted p.adj <= alpha; 1 for all.
permutations: Number of permutations for the tests of passive variables.

Value

A tibble with species, group (the group or combination the species indicates), stat, A (specificity) and B (fidelity; for IndVal only), the permutation p.value and the adjusted p.adj, sorted by group and decreasing stat.

Details

Every species is tested, so with many species some reach p.value < 0.05 by chance. Following De Caceres et al. (2010) and Legendre and Legendre (2012), p-values are corrected for multiple testing before species are selected.

References

Dufrene, M. and Legendre, P. (1997). Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological Monographs, 67, 345-366. doi:10.1890/0012-9615(1997)067[0345:SAAIST]2.0.CO;2

De Caceres, M., Legendre, P. and Moretti, M. (2010). Improving indicator species analysis by combining groups of sites. Oikos, 119, 1674-1684. doi:10.1111/j.1600-0706.2010.18334.x

Examples

ants <- dplyr::mutate(png_ants, unit = paste(site, season, transect),
                      zone = ifelse(elevation <= 700, "lowland", "montane"))
set.seed(1)
beta_indicator(ants, site = unit, group = zone, permutations = 199)
#> # A tibble: 0 x 7
#> # i 7 variables: species <chr>, group <chr>, stat <dbl>, A <dbl>, B <dbl>,
#> #   p.value <dbl>, p.adj <dbl>