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Calculate Confidence Intervals for a Biodiversity Indicator

Source: R/calc_ci_methods.R
calc_ci.Rd

This function calculates bootstrap confidence intervals for a biodiversity indicator. It is called automatically when calculating a biodiversity indicator over time unless you choose 'none' for ci_type.

Usage

calc_ci(x, indicator, ...)

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

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

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

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

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

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

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

# 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 = ci_type, ...)

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

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

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

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.

num_bootstrap

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

ci_type

Type of bootstrap confidence intervals to calculate. (Default: "norm". Select "none" to avoid calculating bootstrap CIs.)

Methods (by class)

  • calc_ci(hill0): Calculate confidence intervals for Hill richness

  • calc_ci(hill1): Calculate confidence intervals for Simpson-Hill diversity

  • calc_ci(hill2): Calculate confidence intervals for Shannon-Hill diversity

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

  • calc_ci(occ_density): Calculate confidence intervals for occurrence 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