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Distance decay of similarity

Source: R/beta.R
beta_decay.Rd

Pairs the pairwise beta diversity from beta_pair() with the distance between sites along a gradient, such as elevation, to study how dissimilarity and its components change with distance.

Usage

beta_decay(
  data,
  gradient,
  site = site,
  species = species,
  abundance = NULL,
  index = c("sorensen", "jaccard", "bray"),
  .by = NULL
)

Arguments

data

A data frame in long format, with one row per record.

gradient

<tidy-select> One or more numeric site attributes, constant within each site. With one column (such as elevation) the distance is the absolute difference; with several (such as c(x, y) coordinates) it is the Euclidean distance.

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.

index

Family of dissimilarity: "sorensen" or "jaccard" (presence and absence) or "bray" (abundance-based Bray-Curtis).

.by

<tidy-select> Optional grouping columns, kept in the output. Grouped data frames are also respected.

Value

A td_beta_decay tibble like the output of beta_pair(), with distance and, for a single gradient column, gradient_1 and gradient_2. Use ggplot2::autoplot() to plot it.

Examples

decay <- beta_decay(png_ants, gradient = elevation, .by = season)
decay
#> # A tibble: 20 x 9
#>    season site_1 site_2 turnover nestedness total gradient_1 gradient_2 distance
#>    <chr>  <chr>  <chr>     <dbl>      <dbl> <dbl>      <int>      <int>    <dbl>
#>  1 dry    MW0200 MW0700    0.667    0.0108  0.677        200        700      500
#>  2 dry    MW0200 MW1200    0.769    0.0239  0.793        200       1200     1000
#>  3 dry    MW0200 MW1700    0.8      0.105   0.905        200       1700     1500
#>  4 dry    MW0200 MW2200    1        0       1            200       2200     2000
#>  5 dry    MW0700 MW1200    0.615    0.0275  0.643        700       1200      500
#>  6 dry    MW0700 MW1700    0.8      0.1     0.9          700       1700     1000
#>  7 dry    MW0700 MW2200    0.833    0.0714  0.905        700       2200     1500
#>  8 dry    MW1200 MW1700    1        0       1           1200       1700      500
#>  9 dry    MW1200 MW2200    0.833    0.0614  0.895       1200       2200     1000
#> 10 dry    MW1700 MW2200    1        0       1           1700       2200      500
#> 11 wet    MW0200 MW0700    0.619    0.0544  0.673        200        700      500
#> 12 wet    MW0200 MW1200    0.8      0.00488 0.805        200       1200     1000
#> 13 wet    MW0200 MW1700    0.9      0.0355  0.935        200       1700     1500
#> 14 wet    MW0200 MW2200    1        0       1            200       2200     2000
#> 15 wet    MW0700 MW1200    0.55     0.075   0.625        700       1200      500
#> 16 wet    MW0700 MW1700    0.9      0.0474  0.947        700       1700     1000
#> 17 wet    MW0700 MW2200    1        0       1            700       2200     1500
#> 18 wet    MW1200 MW1700    0.6      0.133   0.733       1200       1700      500
#> 19 wet    MW1200 MW2200    1        0       1           1200       2200     1000
#> 20 wet    MW1700 MW2200    0.8      0.0667  0.867       1700       2200      500