Calculate Biodiversity Indicators Over Time

This function provides a flexible framework for calculating various biodiversity indicators over time. It prepares the data, creates a grid, calculates indicators, and formats the output into an appropriate S3 object ('indicator_ts'). Specific implementations for different indicator types are provided using the appropriate wrappers.

Usage

# S3 method for class 'obs_richness'
calc_ts(x, ...)

# S3 method for class 'cum_richness'
calc_ts(x, ...)

# S3 method for class 'total_occ'
calc_ts(x, ...)

# S3 method for class 'occ_density'
calc_ts(x, ...)

# S3 method for class 'newness'
calc_ts(x, ...)

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

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

# S3 method for class 'ab_rarity'
calc_ts(x, ...)

# S3 method for class 'area_rarity'
calc_ts(x, ...)

# S3 method for class 'spec_occ'
calc_ts(x, ...)

# S3 method for class 'spec_range'
calc_ts(x, ...)

# S3 method for class 'tax_distinct'
calc_ts(x, set_rows = 1, ...)

# S3 method for class 'occ_turnover'
calc_ts(x, ...)

calc_ts(x, ...)

Arguments

x

A data cube object ('processed_cube').

...

Additional arguments passed to specific indicator calculation functions.

set_rows

Automatically select which taxonomic information to keep when there are multiple options. Default value of 1 keeps the first option, which is usually the best.

Value

An S3 object of the class 'indicator_ts' containing the calculated indicator values and metadata.

Examples

occurrence_density_trend <- occ_density_ts(example_cube_1)
#> [1] "All values of t are equal to  0.00476796992591819 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.0023839849629591 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.0023839849629591 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.0023839849629591 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00240021194277064 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00224909810248931 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00449819620497863 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00240021194277064 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00236802069961937 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00226315716326052 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00452631432652092 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00224909810248931 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00224909810248931 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00226315716326046 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00224909810248929 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00238398496295911 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00899639240995725 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00224909810248931 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00236802069961937 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00223525492979505 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00224909810248931 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00226315716326046 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00229194154160255 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00232164662838182 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00232164662838179 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00464329325676364 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.00240021194277066 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  0.0022631571632605 \n Cannot calculate confidence intervals"
plot(occurrence_density_trend, min_year=1980)