Distance decay with geographic, elevational or environmental distance

Computes pairwise beta diversity with tidydiversity::beta_pair() and joins distances from geo_distance() (great-circle, elevational or environmental), returning a td_beta_decay object (see tidydiversity::beta_decay()) for tidydiversity::beta_decay_model() and ggplot2::autoplot().

Usage

geo_decay(
  data,
  lon = lon,
  lat = lat,
  elevation = NULL,
  site = site,
  species = species,
  abundance = NULL,
  index = c("sorensen", "jaccard", "bray"),
  method = c("haversine", "elevation", "euclidean", "environmental"),
  vars = NULL,
  scale = TRUE,
  metric = c("euclidean", "gower"),
  .by = NULL
)

Arguments

data

A long community table with coordinate columns.

lon, lat, elevation

Coordinate and elevation columns of data.

site, species, abundance

<tidy-select> Site, species and (optional) abundance columns of data.

index

Dissimilarity family passed to tidydiversity::beta_pair(): "sorensen", "jaccard" or "bray".

method, vars, scale, metric

Passed to geo_distance().

.by

<tidy-select> Optional grouping columns.

Value

A td_beta_decay tibble.

Details

Needs the tidydiversity package.

Examples

png_ants <- tidydiversity::png_ants
# Published bait GPS for the Mt Wilhelm sites
sites <- geo_example_sites()
com <- dplyr::left_join(png_ants, sites[c("site", "lon", "lat")],
  by = "site"
)
decay <- geo_decay(com, lon, lat, .by = season, method = "haversine")
head(decay)
#> # A tibble: 6 × 7
#>   season site_1 site_2 turnover nestedness total distance
#>   <chr>  <chr>  <chr>     <dbl>      <dbl> <dbl>    <dbl>
#> 1 dry    MW0200 MW0700    0.667     0.0108 0.677    8802.
#> 2 dry    MW0200 MW1200    0.769     0.0239 0.793    7212.
#> 3 dry    MW0200 MW1700    0.8       0.105  0.905   10931.
#> 4 dry    MW0200 MW2200    1         0      1       17211.
#> 5 dry    MW0700 MW1200    0.615     0.0275 0.643    1978.
#> 6 dry    MW0700 MW1700    0.8       0.1    0.9      3272.