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Calculate Taxonomic Distinctness Over Space or Time

Source: R/indicator_wrappers.R
tax_distinct_map.Rd

This function calculates the taxonomic distinctness index (TDI) over a gridded map or as a time series (see 'Details' for more information).

Usage

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

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)

crs_unit_convert

Force a particular output CRS even when it has different units than the input CRS. (Default: FALSE)

shapefile_path

Path of an external shapefile to merge into the workflow. For example, if you want to calculate your indicator particular features such as protected areas or wetlands.

invert

Calculate an indicator over the inverse of the shapefile (e.g. if you have a protected areas shapefile this would calculate an indicator over all non protected areas)

Value

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

Details

Taxonomic distinctness is an essential biodiversity variable (EBV) that measures the taxonomic relatedness between species, providing a measure of biodiversity that accounts for evolutionary relationships. A distance matrix based on pairwise taxonomic relationships is calculated for each cell using the taxize package (Chamberlain & Szöcs, 2013; Chamberlain et al., 2020), then taxonomic distinctness is calculated as the Taxonomic Distinctness Index (TDI; Clarke & Warwick, 1999): $$ \frac{\sum\sum_{i<j} \frac{|R_i - R_j|}{L}}{\frac{S(S-1)}{2}} $$ where S is the number of species, Ri and Rj are the taxonomic ranks of species i and j (from the GBIF Taxonomic Backbone), and L is the maximum number of taxonomic ranks. The TDI ranges from 0 to 1, with higher values indicating greater taxonomic distinctness.

Functions

  • tax_distinct_map():

  • tax_distinct_ts():

References

Chamberlain, S. A., & Szöcs, E. (2013). taxize: taxonomic search and retrieval in R. F1000Research, 2.

Chamberlain, S., Szoecs, E., Foster, Z., Boettiger, C., Ram, K., Bartomeus, I., Baumgartner, J., O'Donnell, J., Oksanen, J., Tzovaras, B. G., Marchand, P., Tran, V., Salmon, M., Li, G., & Grenié, M. (2020). taxize: Taxonomic Information from Around the Web. R package version 0.9.98. https://github.com/ropensci/taxize.

Clarke, K. R., & Warwick, R. M. (1999). The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels. Marine Ecology Progress Series, 184, 21-29.

See also

compute_indicator_workflow

Examples

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

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