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

total_occurrences_trend <- total_occ_ts(example_cube_1)
#> Spherical geometry (s2) switched off
#> although coordinates are longitude/latitude, st_intersection assumes that they
#> are planar
#> Spherical geometry (s2) switched on
#> Warning: attribute variables are assumed to be spatially constant throughout all geometries
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  3 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  4 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  3 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  67 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  5 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  6 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  4 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
plot(total_occurrences_trend, min_year=1980)