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Bootstrap uncertainty of the isodar-adjusted inequality

Source: R/isoderr.R
isoderr.Rd

Resamples sites with replacement (keeping all habitats of a site together), refits the isodars and recomputes the IAI for each resample. Absent habitats are identified once, on the full data, and kept fixed in every resample.

Usage

isoderr(
  data,
  hab_cols = NULL,
  n_habitats = NULL,
  dim = "pairwise",
  abundances = NULL,
  n_boot = 1000,
  output = c("SD", "SE", "CI"),
  conf_level = 0.95,
  weights = NULL,
  flip_intercept = TRUE,
  min_occupancy = 1,
  max_search = 10000,
  seed = NULL,
  ndim_method = "auto",
  absent = "auto",
  absent_max_count = 0,
  absent_min_sites = 5
)

Arguments

data

A data frame. Wide format: one row per site and one numeric column per habitat; NA marks a habitat that is absent from, or was not sampled at, a site. Long format: one row per species x site x habitat (see Details).

hab_cols

Wide format: character vector of habitat column names.

n_habitats

Alternatively, the number of habitat columns, taken from the start of data. One of hab_cols or n_habitats is required.

dim

"pairwise" or "ndim".

abundances

Numeric vector of total abundances, or NULL for the density-independent value.

n_boot

Number of bootstrap replicates.

output

"SD" or "SE" (both the bootstrap standard deviation, which is the standard error of the estimate) or "CI" (percentile interval).

conf_level

Confidence level for output = "CI".

weights

Pairwise only: NULL (equal weights), "1/var" (inverse variance of each isodar's vertical residuals, \(1/(sd^2(1+b^2))\)), or a numeric vector with one weight per isodar.

flip_intercept

Pairwise only. If TRUE, an isodar with a negative intercept and positive slope is expressed in the reverse direction (habitats swapped), so that intercepts are non-negative.

min_occupancy

Individuals required in every habitat for the density-independent value.

Largest total searched for the density-independent value.

seed

Optional random-number seed.

ndim_method

"auto", "pca" or "latent"; see Details.

absent

Habitats the species does not use: "auto" (detected from the data, see Details), "none", or a character vector of habitat names (character(0) is the same as "none").

absent_max_count, absent_min_sites

Thresholds for absent = "auto"; see Details.

Value

A tibble with total_abundance, niche_breadth (estimate from the full data), uncertainty (SD/SE) or lower and upper (CI), and n_valid (bootstrap replicates that produced a value).

Examples

set.seed(1)
sim <- simulate_isodars(1.5, 1.5, 5, 5, noise = 1, n = 30)
isoderr(sim, hab_cols = c("hab1", "hab2", "hab3"), abundances = 100,
        n_boot = 50, seed = 1)
#> # A tibble: 1 × 4
#>   total_abundance niche_breadth uncertainty n_valid
#>             <dbl>         <dbl>       <dbl>   <dbl>
#> 1             100         0.656     0.00364      50