Calculate Taxonomic Distinctness Over Time

This function calculates the taxonomic distinctness index as a time series.

Usage

tax_distinct_ts(data, rows = 1, ...)

Arguments

data

A data cube object (class 'processed_cube').

rows

Choose which row to select if there are multiple matches when retrieving taxonomic information from GBIF. (Default is 1. Use NA for interactive mode.)

...

Arguments passed on to compute_indicator_workflow

ci_type

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

cell_size

Length of grid cell sides, in km. (Default: 10 for country, 100 for continent or world)

level

Spatial level: 'cube', 'continent', 'country', 'world', 'sovereignty', or 'geounit'. (Default: 'cube')

region

The region of interest (e.g., "Europe"). (Default: "Europe")

ne_type

The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. (Default: "countries")

ne_scale

The scale of Natural Earth data to download: 'small' - 110m, 'medium' - 50m, or 'large' - 10m. (Default: "medium")

output_crs

The CRS you want for your calculated indicator. (Leave blank to let the function choose a default based on grid reference system)

first_year

Exclude data before this year. (Uses all data in the cube by default.)

last_year

Exclude data after this year. (Uses all data in the cube by default.)

spherical_geometry

If set to FALSE, will temporarily disable spherical geometry while the function runs. Should only be used to solve specific issues. (Default is TRUE)

make_valid

Calls st_make_valid() from the sf package. Increases processing time but may help if you are getting polygon errors. (Default is FALSE).

num_bootstrap

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

Value

An S3 object with the classes 'indicator_ts' and 'tax_distinct' containing the calculated indicator values and metadata.

See also

compute_indicator_workflow

Examples

if (FALSE) { # \dontrun{
td_ts <- tax_distinct_ts(example_cube_1, level = "country", region = "Denmark")
plot(td_ts)
} # }