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Calculate Confidence Intervals for a Biodiversity Indicator

Source: R/calc_ci_methods.R
calc_ci.Rd

Calculates indicator-level bootstrap confidence intervals. It is called internally by add_ci() (indicator level) or when ci_type is supplied to a *_ts() function; it is not meant to be called directly.

Usage

calc_ci(x, indicator, ...)

# Default S3 method
calc_ci(x, indicator, ...)

# S3 method for class 'total_occ'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'occ_density'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'spec_richness_density'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'newness'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'williams_evenness'
calc_ci(x, ...)

# S3 method for class 'pielou_evenness'
calc_ci(x, ...)

# S3 method for class 'ab_rarity'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'area_rarity'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'spec_occ'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'spec_range'
calc_ci(x, indicator, num_bootstrap = 1000, ci_type = "perc", ...)

# S3 method for class 'hill0'
calc_ci(x, indicator, num_bootstrap = 1000, ...)

# S3 method for class 'hill1'
calc_ci(x, indicator, num_bootstrap = 1000, ...)

# S3 method for class 'hill2'
calc_ci(x, indicator, num_bootstrap = 1000, ...)

Arguments

x

A data cube object

indicator

An indicator calculated over time, in the form of a data frame. *Note: this should NOT be an 'indicator_ts' object as it is meant to be called by the 'compute_indicator_workflow' function.

...

Additional arguments passed to specific calc_ci functions and on to boot::boot.ci() (e.g., conf, h, hinv), or to the iNEXT-based calculation for Hill numbers (e.g., conf).

num_bootstrap

(Optional) Set the number of bootstraps to calculate for generating confidence intervals. (Default: 1000)

ci_type

(Optional) Type of bootstrap interval passed to boot::boot.ci(). (Default: "perc")

Value

A data frame containing indicator values with calculated lower (ll) and upper (ul) confidence bounds.

Methods (by class)

  • calc_ci(total_occ): Calculate confidence intervals for total occurrences

  • calc_ci(occ_density): Calculate confidence intervals for occurrence density

  • calc_ci(spec_richness_density): Calculate confidence intervals for species richness density

  • calc_ci(newness): Calculate confidence intervals for newness

  • calc_ci(williams_evenness): Calculate confidence intervals for Williams' evenness

  • calc_ci(pielou_evenness): Calculate confidence intervals for Pielou's evenness

  • calc_ci(ab_rarity): Calculate confidence intervals for abundance-based rarity

  • calc_ci(area_rarity): Calculate confidence intervals for area-based rarity

  • calc_ci(spec_occ): Calculate confidence intervals for species occurrences

  • calc_ci(spec_range): Calculate confidence intervals for species range

  • calc_ci(hill0): Calculate confidence intervals for Hill0 (Richness)

  • calc_ci(hill1): Calculate confidence intervals for Hill1 (Shannon)

  • calc_ci(hill2): Calculate confidence intervals for Hill2 (Simpson)

Examples

# \donttest{
# calc_ci() is called automatically when confidence intervals are requested
# during indicator calculation (or by add_ci(bootstrap_level = "indicator"))
occ_ts <- total_occ_ts(example_cube_1, first_year = 2000,
                       ci_type = "perc", num_bootstrap = 100)
head(occ_ts$data)
#> # A tibble: 6 × 9
#>    year diversity_val int_type    ll    ul est_boot se_boot bias_boot  conf
#>   <dbl>         <dbl> <chr>    <dbl> <dbl>    <dbl>   <dbl>     <dbl> <dbl>
#> 1  2000          2166 perc     1866. 2632.    2189.    186.     23.3   0.95
#> 2  2001          2831 perc     2579. 3098.    2820.    137.    -10.9   0.95
#> 3  2002          3366 perc     2988. 3880.    3364.    225.     -2.31  0.95
#> 4  2003          3114 perc     2629. 3722.    3120.    258.      6.15  0.95
#> 5  2004          2934 perc     2534. 3487.    2997.    227.     63.0   0.95
#> 6  2005          4733 perc     3994. 5378.    4770.    329.     36.6   0.95
# }