Bootstrap replicates of diversity estimates

Returns the individual bootstrap replicates behind the standard errors of div_estimate() and div_standardise(), one row per site, order q and replicate. Each replicate is a multinomial sample of the observed size drawn from the estimated community, including undetected species, as in iNEXT (Chao et al. 2014). Use the replicates to carry estimation uncertainty into downstream models, for example by refitting a model to each replicate and pooling the coefficients (see vignette("modelling")).

Usage

div_boot(
  data,
  site = site,
  species = species,
  abundance = NULL,
  q = c(0, 1, 2),
  type = c("asymptotic", "standardised"),
  coverage = NULL,
  size = NULL,
  nboot = 100,
  .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 diversity: any of 0, 1 and 2.

type

"asymptotic" for the asymptotic estimates of div_estimate(), or "standardised" for diversity at a common coverage or size as in div_standardise().

coverage

Target sample coverage between 0 and 1. If both coverage and size are NULL, a default coverage is chosen for each group.

size

Target sample size. Supply either coverage or size.

nboot

Number of bootstrap replicates.

.by

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

Value

A tibble with the grouping columns, the site column, q, .draw (replicate number) and diversity. For type = "standardised", also m, the size each site was standardised to (fixed across replicates).

Examples

set.seed(1)
draws <- div_boot(png_ants, q = 0, .by = season, nboot = 20)
draws
#> # A tibble: 200 x 5
#>    season site       q .draw diversity
#>    <chr>  <chr>  <dbl> <int>     <dbl>
#>  1 dry    MW0200     0     1      16.6
#>  2 dry    MW0200     0     2      16.0
#>  3 dry    MW0200     0     3      20.9
#>  4 dry    MW0200     0     4      31.6
#>  5 dry    MW0200     0     5      20.9
#>  6 dry    MW0200     0     6      19.1
#>  7 dry    MW0200     0     7      18.1
#>  8 dry    MW0200     0     8      20.4
#>  9 dry    MW0200     0     9      18.1
#> 10 dry    MW0200     0    10      16.6
#> # i 190 more rows

# The bootstrap standard error of each site
dplyr::summarise(draws, se = sd(diversity), .by = c(season, site, q))
#> # A tibble: 10 x 4
#>    season site       q    se
#>    <chr>  <chr>  <dbl> <dbl>
#>  1 dry    MW0200     0  6.36
#>  2 wet    MW0200     0 11.0 
#>  3 dry    MW0700     0 24.6 
#>  4 wet    MW0700     0 32.1 
#>  5 dry    MW1200     0 12.7 
#>  6 wet    MW1200     0 15.0 
#>  7 dry    MW1700     0  1.81
#>  8 wet    MW1700     0 15.2 
#>  9 dry    MW2200     0  5.23
#> 10 wet    MW2200     0  3.67