Evenness profiles

Computes the five classes of Hill-number evenness of Chao and Ricotta (2019) for each site, either from the observed sample or from diversity standardised to a common sample coverage, as in iNEXT.4steps.

Usage

div_evenness(
  data,
  site = site,
  species = species,
  abundance = NULL,
  q = seq(0, 2, 0.2),
  class = c("E1", "E2", "E3", "E4", "E5"),
  method = c("estimated", "observed"),
  coverage = NULL,
  conf = 0.95,
  nboot = 50,
  .by = NULL
)

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.

q

Orders of completeness, non-negative numbers. Defaults to a profile from 0 to 2.

class

Evenness classes to return, any of "E1" to "E5".

method

"estimated" (the default) uses diversity standardised to coverage; "observed" uses the observed sample.

coverage

Target coverage for method = "estimated". Defaults to the lowest coverage that every site in a group reaches at twice its sample size.

conf

Confidence level of the intervals.

nboot

Number of bootstrap replicates. Use 0 to skip them.

.by

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

Value

A td_evenness tibble with the grouping columns, the site column, class, q, evenness, se, lower and upper, and coverage for the estimated method.

References

Chao, A. and Ricotta, C. (2019). Quantifying evenness and linking it to diversity, beta diversity, and similarity. Ecology, 100, e02852. doi:10.1002/ecy.2852

Chao, A. et al. (2020). Quantifying sample completeness and comparing diversities among assemblages. Ecological Research, 35, 292-314. doi:10.1111/1440-1703.12102

Examples

div_evenness(png_ants, q = c(0, 1, 2), .by = season, nboot = 0)
#> # A tibble: 150 x 9
#>    season site   class     q evenness    se lower upper coverage
#>    <chr>  <chr>  <chr> <dbl>    <dbl> <dbl> <dbl> <dbl>    <dbl>
#>  1 dry    MW0200 E1        0    1        NA    NA    NA    0.565
#>  2 dry    MW0200 E1        1    0.945    NA    NA    NA    0.565
#>  3 dry    MW0200 E1        2    0.960    NA    NA    NA    0.565
#>  4 dry    MW0200 E2        0    1        NA    NA    NA    0.565
#>  5 dry    MW0200 E2        1    0.945    NA    NA    NA    0.565
#>  6 dry    MW0200 E2        2    0.752    NA    NA    NA    0.565
#>  7 dry    MW0200 E3        0    1        NA    NA    NA    0.565
#>  8 dry    MW0200 E3        1    0.876    NA    NA    NA    0.565
#>  9 dry    MW0200 E3        2    0.752    NA    NA    NA    0.565
#> 10 dry    MW0200 E4        0    1        NA    NA    NA    0.565
#> # i 140 more rows