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Spatially constrained rarefaction

geo_rarefy_spatial.Rd

Accumulates species richness by adding samples in order of increasing distance from a seed sample (spatially contiguous rarefaction), and optionally compares that curve to random-order accumulation. Coverage standardisation (tidydiversity::div_rarefy(), tidydiversity::div_standardise()) remains the default for effort bias; use this verb when you need an aggregation signal along a transect or plot (Chiu 2023; McGlinn et al. 2025).

Usage

geo_rarefy_spatial(
  data,
  lon = lon,
  lat = lat,
  site = site,
  species = species,
  abundance = NULL,
  seed = NULL,
  nperm = 0,
  .by = NULL
)

Arguments

data

Long community table with coordinates and species.

lon, lat, site, species

Coordinate, site and species columns.

abundance

Optional abundance column; presence is used when NULL.

seed

Site id or row index of the starting sample. When NULL, every site is used as a seed and curves are averaged.

nperm

Number of random-order permutations for the null curve.

.by

Optional grouping columns.

Value

A tibble (tmr_geo_rarefy) with n_sites, richness_spatial, and when nperm > 0 also richness_random (mean) and richness_random_sd.

Examples

set.seed(1)
pts <- expand.grid(x = 1:4, y = 1:3)
pts$site <- paste0("s", seq_len(nrow(pts)))
com <- expand.grid(site = pts$site, species = paste0("sp", 1:5),
                   stringsAsFactors = FALSE)
com$abundance <- rpois(nrow(com), 1)
com <- dplyr::left_join(com, pts, by = "site")
geo_rarefy_spatial(com, lon = x, lat = y, nperm = 19)
#> # A tibble: 12 × 4
#>    n_sites richness_spatial richness_random richness_random_sd
#>      <int>            <dbl>           <dbl>              <dbl>
#>  1       1                5               5                  0
#>  2       2                5               5                  0
#>  3       3                5               5                  0
#>  4       4                5               5                  0
#>  5       5                5               5                  0
#>  6       6                5               5                  0
#>  7       7                5               5                  0
#>  8       8                5               5                  0
#>  9       9                5               5                  0
#> 10      10                5               5                  0
#> 11      11                5               5                  0
#> 12      12                5               5                  0