Calculate Biodiversity Indicators Over Space or Time — compute_indicator

This function provides a flexible framework for calculating various biodiversity indicators on a spatial grid or as a time series. It prepares the data, creates a grid, calculates indicators, and formats the output into an appropriate S3 object ('indicator_map' or 'indicator_ts').

Usage

compute_indicator_workflow(
  data,
  type,
  dim_type = c("map", "ts"),
  cell_size = NULL,
  level = c("continent", "country", "world"),
  region = "Europe",
  output_crs = NULL,
  first_year = NULL,
  last_year = NULL,
  spherical_geometry = TRUE,
  make_valid = FALSE,
  ...
)

Arguments

data

A data cube object (class 'processed_cube').

type

The indicator to calculate. Supported options include:

'obs_richness': Observed species richness.
'total_occ': Total number of occurrences.
'newness': Mean year of occurrence.
'density': Density of occurrences.
'williams_evenness', 'pielou_evenness': Evenness measures.
'ab_rarity', 'area_rarity': Abundance-based and area-based rarity scores.

dim_type

Dimension to calculate indicator over (time: 'ts', or space: 'map')

cell_size

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

level

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

region

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

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).

...

Additional arguments passed to specific indicator calculation functions.

Value

An S3 object containing the calculated indicator values and metadata.

Examples

diversity_map <- compute_indicator_workflow(example_cube_1,
                                            type = "obs_richness",
                                            dim_type = "map",
                                            level = "country",
                                            region = "Denmark")
diversity_map
#> Gridded biodiversity indicator map
#> 
#> Name of Indicator: Observed Species Richness 
#> 
#> Map of Denmark 
#> 
#> Projected CRS: EPSG:4326 
#> 
#> Coordinate range:
#>      xmin      ymin      xmax      ymax 
#>  8.121484 54.628857 15.137109 57.736914 
#> 
#> Grid cell size: 0.25 km^2 
#> Number of cells: 168 
#> 
#> Observation years: 1862 - 2023 
#> Total years with observations: 125 
#> 
#> Number of species represented: 106 
#> Number of families represented: 31 
#> 
#> Kingdoms represented: Animalia 
#> 
#> First 10 rows of data (use n = to show more):
#> 
#> # A tibble: 168 × 3
#>    cellid area_km2 diversity_val
#>     <int>   [km^2]         <int>
#>  1     72     446.            32
#>  2     73     446.            34
#>  3     74     446.            47
#>  4     75     446.            48
#>  5     76     446.            37
#>  6     77     446.            21
#>  7     78     446.            33
#>  8     79     446.            32
#>  9     80     446.            29
#> 10     81     446.            41
#> # ℹ 158 more rows