Package {b3gbi}

A value or the magrittr placeholder.

A function call using the magrittr semantics.

An object of class indicator_ts to which confidence intervals should be added.

(Optional) Number of bootstrap replicates to perform. (Default: 1000)

(Optional) Level at which to perform bootstrapping:

• auto (default): Uses cube if the dubicube package is installed, and otherwise falls back to indicator (with a message).

• cube: Bootstrapping is done by resampling the occurrence records in the cube, using the dubicube package. This is statistically more robust as it captures the underlying sampling uncertainty. Requires dubicube.

• indicator: Within each year, the component values of the indicator (occurrence records, species, or grid-cell values) are resampled with boot, without recalculating the indicator from a resampled cube. This is faster for large cubes but less robust, and does not require dubicube.

The level that was used is stored in the ci_method element of the returned object and shown when it is printed.

(Optional) Type of bootstrap confidence intervals to calculate. (Default: "perc"). Supported options are:

• perc: Percentile intervals.

• bca: Bias-corrected and accelerated intervals.

• norm: Normal approximation intervals.

• basic: Basic bootstrap intervals.

• none: No confidence intervals calculated; the indicator is returned unchanged (with a message).

(Optional) A function for transforming the indicator values before calculating confidence intervals (e.g., log). At indicator level it is passed to boot::boot.ci() as h (not used for Hill numbers). The trans/inv_trans arguments are ignored for evenness indicators at cube level, which always use the logit transformation unless overridden via boot_args or ci_args. (Default: identity function)

(Optional) The inverse of the transformation function trans (e.g., exp). Used to back-transform the intervals to the original scale. At indicator level it is passed to boot::boot.ci() as hinv. (Default: identity function)

(Optional) The confidence level for the calculated intervals (e.g., 0.95 for 95% CIs). Used at both bootstrap levels. (Default: 0.95)

(Optional) Logical. If the indicator already contains confidence intervals (ll and ul columns), should they be replaced? (Default: TRUE)

(Optional) Named list of additional arguments passed to dubicube::bootstrap_cube() (cube level only). (Default: list())

(Optional) Named list of additional arguments passed to dubicube::calculate_bootstrap_ci() (cube level only). (Default: list())

(Optional) Integer. Random seed for bootstrapping, used at both bootstrap levels. The random number generator state of the session is restored afterwards. Use NA to not set a seed. (Default: 123)

(Optional) Additional arguments passed to calc_ci() (indicator level only).

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object

An indicator calculated over time, in the form of a data frame. *Note: this should NOT be an 'indicator_ts' object as it is meant to be called by the 'compute_indicator_workflow' function.

Additional arguments passed to specific calc_ci functions and on to boot::boot.ci() (e.g., conf, h, hinv), or to the iNEXT-based calculation for Hill numbers (e.g., conf).

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

(Optional) Type of bootstrap interval passed to boot::boot.ci(). (Default: "perc")

A data cube object ('processed_cube').

Additional arguments passed to specific indicator calculation functions.

Integer controlling the occupancy denominator (default 0):

• 0 — Total-area occupancy: number of grid cells occupied by the species (across all years) / total number of grid cells in the study region (including unsampled cells). Presence-only caveat: empty cells cannot be assumed truly unoccupied; they may simply be unsampled.

• 1 — Relative-to-ever-occupied occupancy: species' cells / cells with at least one occurrence (any species, any year). Conditions on cells where sampling effort is documented.

• 2 — Temporal mean annual occupancy: for each year, compute the proportion of that year's occupied cells (any species) in which the species was recorded; then average those annual proportions across the years in which the species was recorded (years without records of the species do not contribute a zero). This captures how consistently a species occupies the active sampling footprint over time.

Note on presence-only data: All three types rely on presence-only records. A cell with no records cannot be assumed to be truly unoccupied. Types 1 and 2 condition on cells with documented occurrences, but those still reflect sampling effort rather than true species absence.

Note on cell aggregation: When a coarser cell_size is chosen, data are aggregated to coarser grid cells before this calculation. All denominators count post-aggregation cells (cellid).

(Optional) If set, only shows values above this (e.g. 1970). Values below the minimum will be replaced with NA. This can be useful e.g. if you have outlier cells where the data is very old causing the legend gradient to stretch in a way that makes other cell values difficult to discern.

A data cube object ('processed_cube').

Additional arguments passed to specific indicator calculation functions.

Integer controlling the occupancy denominator (default 0):

• 0 — Total-area occupancy: number of cells occupied by species / total number of grid cells in the study region (including unsampled cells). This is the most conservative measure. Presence-only caveat: empty cells cannot be assumed to be truly unoccupied; they may simply lack sampling effort.

• 1 — Relative-to-ever-occupied occupancy: number of cells occupied by species / number of cells with at least one occurrence (any species) anywhere in the time window. This conditions on cells where some sampling effort is documented but the denominator is still constant across years.

• 2 — Annual occupancy: for each year, number of cells occupied by species / number of cells with at least one occurrence (any species) in that year. The denominator therefore varies by year, reflecting changes in sampling footprint over time.

Note on presence-only data: All three types are computed from presence-only occurrence data. A cell with no records cannot be assumed to be truly unoccupied; it may be unsampled or under-surveyed. Types 1 and 2 partially address this by restricting the denominator to cells with documented occurrences, but they still reflect recording effort rather than true absence. Interpret all types with care.

Note on cell aggregation: When a coarser cell_size is chosen, data are aggregated to coarser grid cells before this calculation. The denominator counts post-aggregation cells (cellid), not original cube cells (cellCode).

Deprecated and ignored. Taxa are now looked up by their GBIF taxon key, so there is no ambiguity to resolve.

A data cube object (class 'processed_cube').

(Optional) Minimum amount of data required for a grid cell or year to be included. For maps, grid cells with fewer than cutoff_length species are removed. For time series, years whose species-by-cell incidence matrix has cutoff_length entries or fewer are removed (with gridded_average = TRUE: coarse grid cells containing cutoff_length or fewer native cells with records that year). Default is 5.

(Optional, maps only) The type of data: "incidence" or "abundance". Default is "incidence".

(Optional, maps only) Whether to assume frequency data if using incidence. Default is FALSE.

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

(Optional, time series only) If TRUE, completeness is calculated separately for each cell of a grid coarser than the cube (using the native cube cells within it as sampling units), and the yearly value is the mean over these grid cells, rather than calculating it for the entire area at once. If cell_size is left at its default ("grid"), a grid 4 times coarser than the cube's resolution is used; otherwise cell_size must be coarser than the cube's resolution. Default is FALSE.

A data cube object (class 'processed_cube', 'processed_cube_dsinfo' or 'sim_cube').

The indicator to calculate. Supported options include:

• 'obs_richness': Observed species richness.

• 'total_occ': Total number of occurrences.

• 'newness': Mean year of occurrence.

• 'occ_density': Density of occurrences.

• 'spec_richness_density': Species richness density (richness / area).

• 'williams_evenness', 'pielou_evenness': Evenness measures.

• 'ab_rarity', 'area_rarity': Abundance-based and area-based rarity scores.

• 'cum_richness': Cumulative species richness.

• 'occ_turnover': Occupancy turnover.

• 'spec_range': Species range size.

• 'spec_occ': Species occurrences.

• 'relative_occupancy': Species relative occupancy.

• 'tax_distinct': Taxonomic distinctness.

• 'hill0': Species richness (estimated by coverage-based rarefaction).

• 'hill1': Hill-Shannon diversity (estimated by coverage-based rarefaction).

• 'hill2': Hill-Simpson diversity (estimated by coverage-based rarefaction).

• 'completeness': Sample completeness (Sample Coverage).

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

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

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

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

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

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

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

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

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

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

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

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

(optional) 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 within your cube). Default is FALSE.

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

Additional arguments passed to specific indicator calculation functions. For time series, ci_type (default "none") and num_bootstrap (default 0) can be used to request bootstrapped confidence intervals directly (alternatively, use add_ci() afterwards). Other examples are newness_min_year for newness_map() and occ_type for relative_occupancy_map() and relative_occupancy_ts().

A character vector of EQDGC cell codes giving the longitude and latitude of a 1-degree cell (e.g. "E009N57" or "W010S34"), optionally followed by up to six letters A-D for sub-cells (e.g. "E009N57DD" = 0.25 degree cell).

A data frame with numeric columns xcoord (easting), ycoord (northing) and utmzone, and a character column hemisphere ("S" for the southern hemisphere; any other value is treated as northern).

(Optional) The EPSG code or CRS string for the desired output CRS. If NULL, the CRS of the first UTM zone will be used.

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A list of objects of class "boot" per year.

(Optional) The temporal list names of bootstrap_list (e.g., year, month ...) containing time point values. Default year.

Additional argument to be passed to the boot::boot.ci() function.

An "indicator_map", "indicator_ts" or "processed_cube" object.

A data cube object (class 'processed_cube').

(Optional) The sample coverage value for the estimator. Default is 0.95.

(Optional) Minimum amount of data required, to avoid errors in the estimation. For maps, grid cells with fewer than cutoff_length species are removed. For time series, years whose species-by-cell incidence matrix has cutoff_length entries or fewer are removed. Default is 5.

(Optional, maps only) If set to "incidence", occurrences are converted to incidence data. Observations are treated as presence/absence and years are used as sampling units. The number of years in which a species was observed within a grid cell are then summarized. If set to "abundance", occurrences are summed across years for each species as a proxy for abundance. Default is "incidence".

(Optional, maps only) If TRUE, the sum of observations for a species within a grid cell is assumed to be a sum of sampling sites in which that species was observed. The maximum number of observations for any species within a grid cell is then taken as a proxy for the total number of sampling sites for that cell. This parameter is ignored if data_type is set to "abundance". It is advisable to leave this on FALSE unless you are certain of how your data is structured. Default is FALSE.

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

(Optional, time series only) Confidence level for bootstrap confidence intervals. Only used when num_bootstrap > 0 and ci_type is not "none" (passed via ...). Default is 0.95.

A biodiversity data object containing species names (either in a data slot or a species_names vector).

A data frame with at least three columns: cellCode (MGRS codes; the first three characters give the UTM zone and latitude band), and xcoord/ycoord (UTM easting and northing).

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

An 'indicator_map' object containing multi-species indicator values associated with map grid cells. This is a required parameter with no default.

(Optional) Plot title. Replace "auto" with your own title if you want a custom title or if calling the function manually.

(Optional) Text for automatic title generation, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) Default label for the legend, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) Custom longitude limits in decimal degrees (WGS84), as c(min, max). Should be supplied together with ylims. If only xlims is supplied, the values are instead interpreted in the units of the indicator_map's coordinate reference system and combined with the map's own y limits.

(Optional) Custom latitude limits in decimal degrees (WGS84), as c(min, max). Should be supplied together with xlims. If only ylims is supplied, the values are instead interpreted in the units of the indicator_map's coordinate reference system and combined with the map's own x limits.

(Optional) Scale transformation for the fill gradient. Can be any transformation accepted by ggplot2::scale_fill_gradient() (e.g., 'log', 'log10' or 'sqrt'), or one of the special values 'boxcox', 'modulus' or 'yj' (Yeo-Johnson), which use the power parameter given in bcpower.

(Optional) Power parameter for the Box-Cox, modulus, or Yeo-Johnson transformations (used only when trans is 'boxcox', 'modulus' or 'yj').

(Optional) Break points for the legend scale.

(Optional) Labels for legend scale break points.

(Optional) Coordinate Reference System (CRS) for the output map. Can be specified as an EPSG code (e.g., 4326) or a proj4string. If NULL (default), the original CRS of the indicator_map object will be used.

(Optional) If TRUE, the grid will determine the edges of the map. If FALSE, a buffer will be added around the grid. If NULL (default), will be set to TRUE if map_level is "cube", otherwise FALSE.

(Optional) If TRUE, the map extent is set to the bounding box of the region that was specified when calculating the indicator_map (e.g. the country or continent), instead of the extent of the grid. This requires that a region was specified, i.e. that the indicator_map was not calculated with level = "cube" or level = "world". Default is FALSE.

(Optional) Colour for the ocean (plot background) outside of the grid. Default is "#92c5f0" (light blue).

(Optional) Colour for the land area outside of the grid. Default is "grey85".

(Optional) Colour for empty grid cells (non-empty grid cells will be coloured according to their indicator value). Default is "transparent".

(Optional) Colour for the grid lines. Default is "black". If visible_gridlines is set to FALSE, this setting will have no effect.

(Optional) Width of the grid lines. If NULL (default), 0.5 for ISEA3H grids and 0.1 otherwise.

(Optional) Transparency of the grid fill colour for empty grid cells (0 = fully transparent, 1 = fully opaque). If visible_gridlines is set to TRUE, default is 0.2. Otherwise, default is 0. Note that this setting does NOT apply to grid cells with indicator values, and has no visible effect while grid_fill_colour is "transparent".

(Optional) Transparency of the grid line colour (0 = fully transparent, 1 = fully opaque). Default is 0.5. If visible_gridlines is set to FALSE, this setting will have no effect. *Note that this setting does NOT apply to the grid outline!

(Optional) Title for the plot legend.

(Optional) Limits for the legend scale.

(Optional) Maximum legend title length before wrapping to a new line.

(Optional) Maximum title length before wrapping to a new line.

(Optional) Show gridlines between cells. Default is TRUE.

(Optional) Show ggplot panel gridlines. Default is FALSE.

(Optional) Factor to expand the map limits beyond the grid limits. This does NOT expand the boundaries of the plot, it only affects where the crop is applied. If this value is too small, some land may be visibly cut off due to map distortion caused by projections. A larger value will extend the bounding box for cropping to prevent this. Must be a positive number. Default is 0.1. This should be enough for most projections, but you can increase this value if you are using an extreme projection and find that some land is visibly cut off.

(Optional) Additional rnaturalearth layers to plot, e.g. c("reefs", "playas").

(Optional) Outline colours for the additional layers, given in the same order as 'layers' (one colour per layer; must be the same length as 'layers'). If NULL (default), all layer outlines are black.

(Optional) Fill colours for the additional layers, given in the same order as 'layers' (must be the same length as 'layers'). If NULL (default), layers are unfilled, except "ocean" and "lakes", which are filled light blue.

(Optional) Scale of Natural Earth data ("small", "medium", or "large"). Default is 'medium'.

(Optional) If TRUE, removes geographical outliers from the plot extent using an Interquartile Range (IQR) method based on the centroid coordinates of the indicator_map cells. This is particularly useful for discrete global grids like ISEA3H where stray data points from coordinate errors can force the map bounds to expand globally. Default is FALSE.

An 'indicator_map' object containing multi-species indicator values associated with map grid cells. This is a required parameter with no default.

(Optional) Legend title. Add your own custom legend title if you don't like the automatically generated one. If set to the default of NULL, the function will provide a legend title based on the indicator being plotted.

(Optional) Change the transparency of the grid fill. Default is 0.8. A value of 0 is full transparency, 1 is solid fill.

(Optional) Filter out NA values so NA grid cells do not appear. Default is TRUE.

(Optional) A list of basemaps you want mapview to display as options to select from. The first one in the list will be shown when the map loads. Default is c("OpenStreetMap", "OpenTopoMap", "CartoDB.Positron", "Esri.WorldImagery").

(Optional) Additional arguments passed to mapview::mapview().

An 'indicator_map' object containing indicator values for individual species associated with map grid cells. This object is typically created using the spec_occ_map(), spec_range_map() or relative_occupancy_map() functions. This is a required parameter with no default.

Species you want to map. Can be either numerical taxonKeys or species names. Partial species names can be given as the beginning of a name (prefix match). This is a required parameter with no default.

(Optional) If TRUE, all species maps will be combined into a single multi-panel plot. Set this to FALSE to plot each species separately. Default is TRUE.

(Optional) Plot title. Replace "auto" with your own title if you want a custom title or if calling the function manually.

(Optional) Text for automatic title generation, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) Default label for the legend, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) Do not show legend. This defaults to FALSE but will be forcibly set to TRUE when plotting species ranges, as all cell values are 1.

(Optional) Custom longitude limits in decimal degrees (WGS84), as c(min, max). Should be supplied together with ylims. If only xlims is supplied, the values are instead interpreted in the units of the indicator_map's coordinate reference system and combined with the map's own y limits.

(Optional) Custom latitude limits in decimal degrees (WGS84), as c(min, max). Should be supplied together with xlims. If only ylims is supplied, the values are instead interpreted in the units of the indicator_map's coordinate reference system and combined with the map's own x limits.

(Optional) Scale transformation for the fill gradient. Can be any transformation accepted by ggplot2::scale_fill_gradient() (e.g., 'log', 'log10' or 'sqrt'), or one of the special values 'boxcox', 'modulus' or 'yj' (Yeo-Johnson), which use the power parameter given in bcpower.

(Optional) Power parameter for the Box-Cox, modulus, or Yeo-Johnson transformations (used only when trans is 'boxcox', 'modulus' or 'yj').

(Optional) Break points for the legend scale.

(Optional) Labels for legend scale break points.

(Optional) Coordinate Reference System (CRS) for the output map. Can be specified as an EPSG code (e.g., 4326) or a proj4string. If NULL (default), the original CRS of the indicator_map object will be used.

(Optional) If TRUE, the grid will determine the edges of the map. If FALSE, a buffer will be added around the grid. If NULL (default), will be set to TRUE if map_level is "cube", otherwise FALSE.

(Optional) If TRUE, the map extent is set to the bounding box of the region that was specified when calculating the indicator_map (e.g. the country or continent), instead of the extent of the grid. This requires that a region was specified, i.e. that the indicator_map was not calculated with level = "cube" or level = "world". Default is FALSE.

(Optional) Colour for the ocean (plot background) outside of the grid. Default is "#92c5f0" (light blue).

(Optional) Colour for the land area outside of the grid. Default is "grey85".

(Optional) Colour for empty grid cells (non-empty grid cells will be coloured according to their indicator value). Default is "transparent".

(Optional) Colour for the grid lines. Default is "black". If visible_gridlines is set to FALSE, this setting will have no effect.

(Optional) Width of the grid lines. If NULL (default), 0.5 for ISEA3H grids and 0.1 otherwise.

(Optional) Transparency of the grid fill colour for empty grid cells (0 = fully transparent, 1 = fully opaque). If visible_gridlines is set to TRUE, default is 0.2. Otherwise, default is 0. Note that this setting does NOT apply to grid cells with indicator values, and has no visible effect while grid_fill_colour is "transparent".

(Optional) Transparency of the grid line colour (0 = fully transparent, 1 = fully opaque). Default is 0.5. If visible_gridlines is set to FALSE, this setting will have no effect. *Note that this setting does NOT apply to the grid outline!

(Optional) Title for the plot legend.

(Optional) Limits for the legend scale.

(Optional) Maximum legend title length before wrapping to a new line.

(Optional) Maximum title length before wrapping to a new line.

(Optional) Maximum species name length before wrapping to a new line. Default: 40 characters.

(Optional) Show gridlines between cells. Default is TRUE.

(Optional) Show ggplot panel gridlines. Default is FALSE.

(Optional) Factor to expand the map limits beyond the grid limits. This does NOT expand the boundaries of the plot, it only affects where the crop is applied. If this value is too small, some land may be visibly cut off due to map distortion caused by projections. A larger value will extend the bounding box for cropping to prevent this. Must be a positive number. Default is 0.5. You can increase this value if you are using an extreme projection and find that some land is visibly cut off.

(Optional) Additional rnaturalearth layers to plot, e.g. c("reefs", "playas").

(Optional) Outline colours for the additional layers, given in the same order as 'layers' (one colour per layer; must be the same length as 'layers'). If NULL (default), all layer outlines are black.

(Optional) Fill colours for the additional layers, given in the same order as 'layers' (must be the same length as 'layers'). If NULL (default), layers are unfilled, except "ocean" and "lakes", which are filled light blue.

(Optional) Scale of Natural Earth data ("small", "medium", or "large"). Default is 'medium'.

(Optional) If TRUE, removes geographical outliers from the plot extent using an Interquartile Range (IQR) method based on the centroid coordinates of the indicator_map cells. This is particularly useful for discrete global grids like ISEA3H where stray data points from coordinate errors can force the map bounds to expand globally. Default is FALSE.

An 'indicator_ts' object containing time series of indicator values matched to species names and/or taxon keys, created using the spec_occ_ts(), spec_range_ts() or relative_occupancy_ts() functions. This is a required parameter with no default.

Species you want to plot. Can be either numerical taxonKeys or species names. Partial species names can be given as the beginning of a name (prefix match). This is a required parameter with no default.

(Optional) If TRUE (default), all species time series will be combined into a single multi-panel plot. Set this to FALSE to plot each species separately.

(Optional) Earliest year to include in the plot.

(Optional) Latest year to include in the plot.

(Optional) Plot title. Replace "auto" with your own title if you want a custom title or if calling the function manually.

(Optional) Text for automatic title generation, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) Default label for the y-axis, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) If TRUE, suppresses y-axis tick labels. Default is FALSE.

(Optional) If TRUE, plot a smoothed trendline over time (stats::loess()). Default is TRUE.

(Optional) Colour for the indicator line or points. Default is darkorange.

(Optional) Transparency for indicator line or points. Default is 0.8.

(Optional) Colour for the bootstrapped confidence intervals. Default is goldenrod1. Set to "NA" if you don't want to plot the CIs.

(Optional) Transparency for indicator confidence interval ribbon (if ci_type = "ribbon"). Default is 0.2.

(Optional) Transparency for indicator error bars (if ci_type = "error_bars"). Default is 1.

(Optional) Colour for the smoothed trendline. Default is blue.

(Optional) Transparency for the smoothed trendline. Default is 0.5.

(Optional) Colour for the uncertainty envelope. Default is "lightsteelblue1".

(Optional) Transparency for the smoothed trendline envelope. Default is 0.2.

(Optional) Transparency for the smoothed lines forming the edges of the trendline envelope. Default is 1.

(Optional) Whether to plot the indicator as a line or a series of points. Options are "line" or "point". Default is "point".

(Optional) Size of the points if point_line = "point". Default is 2.

(Optional) Width of the line if point_line = "line". Default is 1.

(Optional) Whether to plot bootstrapped confidence intervals as a "ribbon" or "error_bars". Default is "error_bars".

(Optional) Width of error bars if ci_type = "error_bars". Default is 1. Note that unlike the default 'width' parameter in geom_errorbar, 'error_width' is NOT dependent on the number of data points in the plot. It is automatically scaled to account for this. Therefore the width you select will be consistent relative to the plot width even if you change 'min_year' and 'max_year'.

(Optional) Thickness of error bars if ci_type = "error_bars". Default is 1.

(Optional) Type of line to plot for smoothed trendline. Options are "solid", "dashed", "dotted", "dotdash", "longdash" or "twodash". Default is "solid".

(Optional) Line width for smoothed trendline. Default is 1.

(Optional) Line width for smoothed trendline confidence intervals. Default is 1.

(Optional) If TRUE, hides gridlines.

(Optional) Label for the x-axis.

(Optional) Label for the y-axis.

(Optional) Expansion factor to expand the x-axis beyond the data. Left and right values are required in the form of c(0.1, 0.2) or simply 0.1 to apply the same value to each side. Default is 0.1.

(Optional) Expansion factor to expand the y-axis beyond the data. Lower and upper values are required in the form of c(0.1, 0.2) or simply 0.1 to apply the same value to the top and bottom. Default is 0.1.

(Optional) Integer giving desired number of breaks for x axis. (May not return exactly the number requested.) Default is 10.

(Optional) Integer giving desired number of breaks for y axis. (May not return exactly the number requested.) Default is 6.

(Optional) Maximum title length before wrapping to a new line.

(Optional) Maximum species name length before wrapping to a new line. Default is 40.

An 'indicator_ts' object containing a time series of multi-species indicator values. This is a required parameter with no default.

(Optional) Earliest year to include in the plot.

(Optional) Latest year to include in the plot.

(Optional) Plot title. Replace "auto" with your own title if you want a custom title or if calling the function manually.

(Optional) Text for automatic title generation, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) Default label for the y-axis, provided by an appropriate S3 method (if calling the function manually, leave as NULL).

(Optional) If TRUE, suppresses y-axis tick labels. Default is FALSE.

(Optional) If TRUE, plot a smoothed trendline over time (stats::loess()). Default is TRUE.

(Optional) Colour for the indicator line or points. Default is darkorange.

(Optional) Transparency for indicator line or points. Default is 0.8.

(Optional) Colour for the bootstrapped confidence intervals. Default is goldenrod1. Set to "NA" if you don't want to plot the CIs.

(Optional) Transparency for indicator confidence interval ribbon (if ci_type = "ribbon"). Default is 0.2.

(Optional) Transparency for indicator error bars (if ci_type = "error_bars"). Default is 1.

(Optional) Colour for the smoothed trendline. Default is blue.

(Optional) Transparency for the smoothed trendline. Default is 0.5.

(Optional) Colour for the uncertainty envelope. Default is "lightsteelblue1".

(Optional) Transparency for the smoothed trendline envelope. Default is 0.2.

(Optional) Transparency for the smoothed lines forming the edges of the trendline envelope. Default is 1.

(Optional) Whether to plot the indicator as a line or a series of points. Options are "line" or "point". Default is "point".

(Optional) Size of the points if point_line = "point". Default is 2.

(Optional) Width of the line if point_line = "line". Default is 1.

(Optional) Whether to plot bootstrapped confidence intervals as a "ribbon" or "error_bars". Default is "error_bars".

(Optional) Width of error bars if ci_type = "error_bars". Default is 1. Note that unlike the default 'width' parameter in geom_errorbar, 'error_width' is NOT dependent on the number of data points in the plot. It is automatically scaled to account for this. Therefore the width you select will be consistent relative to the plot width even if you change 'min_year' and 'max_year'.

(Optional) Thickness of error bars if ci_type = "error_bars". Default is 1.

(Optional) Type of line to plot for smoothed trendline. Options are "solid", "dashed", "dotted", "dotdash", "longdash" or "twodash". Default is "solid".

(Optional) Line width for smoothed trendline. Default is 1.

(Optional) Line width for smoothed trendline confidence intervals. Default is 1.

(Optional) If TRUE, hides gridlines.

(Optional) Label for the x-axis.

(Optional) Label for the y-axis.

(Optional) Expansion factor to expand the x-axis beyond the data. Left and right values are required in the form of c(0.1, 0.2) or simply 0.1 to apply the same value to each side. Default is 0.1.

(Optional) Expansion factor to expand the y-axis beyond the data. Lower and upper values are required in the form of c(0.1, 0.2) or simply 0.1 to apply the same value to the top and bottom. Default is 0.1.

(Optional) Integer giving desired number of breaks for x axis. (May not return exactly the number requested.) Default is 10.

(Optional) Integer giving desired number of breaks for y axis. (May not return exactly the number requested.) Default is 6.

(Optional) Maximum title length before wrapping to a new line.

A list describing the indicator. Must contain at least div_type and raw_data.

Integer. Number of bootstrap samples.

Character. Type of confidence interval.

Optional integer. Random seed for bootstrapping. (Default: 123)

Optional transformation function applied to the statistic. Will be overridden if specified by the indicator rule book.

Optional inverse transformation function. Will be overridden if specified by the indicator rule book.

Numeric between 0 and 1. Confidence level.

(Optional) Vector of years expected in the output. Used to ensure consistent data frame structure during bootstrapping.

Named list of additional arguments passed to bootstrap_cube(), overriding defaults.

Named list of additional arguments passed to calculate_bootstrap_ci(), overriding defaults.

Object of class available_indicators

(Optional) Number of indicators to print (default 30).

Currently unused.

An indicator_map object.

Integer specifying the number of rows of data to display.

Logical. If TRUE, includes rows with NA diversity values in the printed output. Default is FALSE.

Additional arguments passed to print().

An indicator_ts object.

(Optional) Integer specifying the number of rows of data to display.

Additional arguments passed to print().

A processed_cube object.

(Optional) Integer specifying the number of rows of cube data to display.

Additional arguments passed to print().

A processed_cube_dsinfo object.

(Optional) Integer specifying the number of rows of data to display.

Additional arguments passed to print().

A sim_cube object.

(Optional) Integer specifying the number of rows of cube data to display.

Additional arguments passed to print().

Either the path to a data cube CSV file (e.g. system.file("extdata", "denmark_mammals_cube_eqdgc.csv", package = "b3gbi")) or a data frame containing the cube.

(Optional) The grid reference system your cube uses. One of "automatic" (default), "eea", "mgrs", "eqdgc", "isea3h", "custom" or "none". With "automatic" the function attempts to detect the grid from the cell codes and returns an error if it fails. If you want to perform analysis on a cube with custom grid codes (e.g. output from the gcube package) or a cube without grid codes, select "custom" or "none", respectively.

(Optional) The first year of occurrences to include. If not specified, uses the earliest year present in the cube.

(Optional) The final year of occurrences to include. If not specified, uses the latest year present in the cube.

(Optional) Logical. If TRUE, skips the check that cell codes match the expected format of grid_type. Not recommended; invalid codes may cause downstream errors. Default FALSE.

(Optional) The name of the column containing the year of occurrence (if something other than 'year'). This column is required unless you have a yearMonth column.

(Optional) The name of the column containing the year and month of occurrence (if present and if other than 'yearMonth'). Use this only if you do not have a year column. The b3gbi package does not use month data, so the function will convert your yearMonth column to a year column.

(Optional) The name of the column containing the year, month and day of occurrence (if present and if other than 'yearMonthDay'). Use this only if you do not have year or yearMonth columns. The b3gbi package does not use day or month data, so the function will convert your yearMonthDay column to a year column.

(Optional) The name of the column containing the grid reference codes (if other than 'cellCode'). This column is required.

(Optional) The name of the column containing the number of occurrences (if other than 'occurrences'). This column is required.

(Optional) The name of the column containing the scientific name of the species (if other than 'scientificName'). Note that it is not necessary to have both a species column and a scientificName column. One or the other is sufficient.

(Optional) The name of the column containing the minimum coordinate uncertainty of the occurrences (if other than 'minCoordinateUncertaintyInMeters').

(Optional) The name of the column containing the minimum temporal uncertainty of the occurrences (if other than 'minTemporalUncertainty').

(Optional) The name of the column containing the kingdom the occurring species belongs to (if other than 'kingdom').

(Optional) The name of the column containing the family the occurring species belongs to (if other than 'family').

(Optional) The name of the column containing the name of the occurring species (if other than 'species'). Note that it is not necessary to have both a species column and a scientificName column. One or the other is sufficient.

(Optional) The name of the column containing the kingdom key of the occurring species (if other than 'kingdomKey').

(Optional) The name of the column containing the family key of the occurring species (if other than 'familyKey').

(Optional) The name of the column containing the species key of the occurring species (if other than 'speciesKey'). The column is required, but note that if you have a 'taxonKey' column you can provide it as the speciesKey.

(Optional) The name of the column containing the occurrence count by family.

(Optional) The name of the column containing the sex of the observed individuals.

(Optional) The name of the column containing the life stage of the observed individuals.

(Optional) The column-separating character in your csv file. This should be automatically recognized, so only specify this if you are having trouble.

A data cube object (class 'processed_cube').

Integer controlling the occupancy denominator. One of:

• 0 (default) - Total-area occupancy: denominator is all grid cells in the study region (including those with no records).

• 1 - Ever-occupied occupancy: denominator is the number of cells with at least one occurrence (any species) anywhere in the time window.

• 2 - Annual occupancy: for time series, the denominator is the number of cells with at least one occurrence (any species) in that year; for maps, the per-year proportion is computed and then averaged across the years in which the species was recorded.

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

An indicator_map or indicator_ts object containing a diversity_val column with NA values to replace.

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A processed_cube object containing taxonomic information in object$data.

A character string specifying the taxonomic rank to group by (e.g., "family", "kingdom"). This column must exist in object$data.

A data cube object (class 'processed_cube').

Deprecated and ignored. Taxa are now looked up by their GBIF taxon key, so there is no ambiguity to resolve.

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)

A data cube object (class 'processed_cube').

Arguments passed on to compute_indicator_workflow

cell_size

(Optional) Length of grid cell sides, in km or degrees. Only used for maps and for time series that require a grid.

• "grid" (default): use the native resolution of the cube. If this would produce more than about 1 million grid cells over the study area (for degree-based cubes: if the resolution is finer than 1 degree for 'world' or 'continent', or finer than 0.1 degrees otherwise), you are asked to confirm in an interactive session, and the function stops with an error in a non-interactive session.

• "auto": determined automatically. For km-based grids it depends on the area of the study region: 100 km for areas of at least 1 million sq km, 10 km for at least 10,000 sq km, 1 km for at least 100 sq km, and 0.1 km for smaller areas. For degree-based grids it is 1 degree for 'world' or 'continent' and 0.1 degrees otherwise. The automatic size is never smaller than the cube's resolution.

• A number (in the units of the cube's resolution, i.e. km or degrees), or for km-based grids a string such as "10km" or "500m".

A manually selected cell size must be a whole number multiple of the cube's resolution.

level

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

region

(Optional) The region of interest (e.g., "Denmark"). Ignored if level is 'cube' or 'world'. (Default: "Europe")

ne_type

(Optional) The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. This parameter is ignored if level is set to 'cube' or 'world'. (Default: "countries")

ne_scale

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

output_crs

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

first_year

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

last_year

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

spherical_geometry

(Optional) 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

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

shapefile_path

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

shapefile_crs

(Optional) CRS of a .wkt shapefile. If your shapefile is .wkt and you do NOT use this parameter, the CRS will be assumed to be EPSG:4326 and the coordinates will be read in as lat/long. If your shape is NOT a .wkt the CRS will be determined automatically.

invert

(optional) 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 within your cube). Default is FALSE.

include_land

(Optional) Include occurrences which fall within the land area. Default is TRUE. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually terrestrial. Grid cells which fall partially on land and partially on ocean will be included even if include_land is FALSE. To exclude terrestrial and/or freshwater taxa, you must manually filter your data cube before calculating your indicator.

include_ocean

(Optional) Include occurrences which fall outside the land area. Default is TRUE. Set as "buffered_coast" to include a set buffer size around the land area rather than the entire ocean area. Note that this is purely a geographic filter, and does not filter based on whether the occurrence is actually marine. Grid cells which fall partially on land and partially on ocean will be included even if include_ocean is FALSE. To exclude marine taxa, you must manually filter your data cube before calculating your indicator.

buffer_dist_km

(Optional) The distance to buffer around the land if include_ocean is set to "buffered_coast". Default is 50 km.

force_grid

(Optional) Forces the calculation of a grid even if this would not normally be part of the pipeline, i.e. for time series. A grid is needed for time series of area-based rarity, Hill diversity and relative occupancy (and for completeness with gridded_average = TRUE). This is switched on automatically for these indicators: the wrappers area_rarity_ts(), hill0_ts(), hill1_ts() and hill2_ts() already set force_grid = TRUE, so do not pass it to them. (Default: FALSE)