Calculate Total Occurrences Over Space or Time

This function calculates the total number of species occurrence records over a gridded map or as a time series (see 'Details' for more ' information).

Usage

total_occ_map(data, ...)

total_occ_ts(data, ...)

Arguments

data

A data cube object (class 'processed_cube').

...

Arguments passed on to compute_indicator_workflow

ci_type: Type of bootstrap confidence intervals to calculate. (Default: "norm". Select "none" to avoid calculating bootstrap CIs.)
cell_size: Length of grid cell sides, in km. (Default: 10 for country, 100 for continent or world)
level: Spatial level: 'cube', 'continent', 'country', 'world', 'sovereignty', or 'geounit'. (Default: 'cube')
region: The region of interest (e.g., "Europe"). (Default: "Europe")
ne_type: The type of Natural Earth data to download: 'countries', 'map_units', 'sovereignty', or 'tiny_countries'. (Default: "countries")
ne_scale: The scale of Natural Earth data to download: 'small' - 110m, 'medium' - 50m, or 'large' - 10m. (Default: "medium")
output_crs: The CRS you want for your calculated indicator. (Leave blank to let the function choose a default based on grid reference system)
first_year: Exclude data before this year. (Uses all data in the cube by default.)
last_year: Exclude data after this year. (Uses all data in the cube by default.)
spherical_geometry: If set to FALSE, will temporarily disable spherical geometry while the function runs. Should only be used to solve specific issues. (Default is TRUE)
make_valid: Calls st_make_valid() from the sf package. Increases processing time but may help if you are getting polygon errors. (Default is FALSE).
num_bootstrap: Set the number of bootstraps to calculate for generating confidence intervals. (Default: 1000)
crs_unit_convert: Force a particular output CRS even when it has different units than the input CRS. (Default: FALSE)
shapefile_path: Path of an external shapefile to merge into the workflow. For example, if you want to calculate your indicator particular features such as protected areas or wetlands.
invert: Calculate an indicator over the inverse of the shapefile (e.g. if you have a protected areas shapefile this would calculate an indicator over all non protected areas)

Value

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

Details

The total number of occurrences is calculated by summing the occurrences of all species observed for each cell or year. While not itself an indicator, this variable provides an overview of the comprehensiveness and distribution of data in the cube being analysed, and may be helpful, or even vital, for interpreting the results of calculated indicators.

Functions

total_occ_map():
total_occ_ts():

Examples

if (FALSE) { # \dontrun{
to_map <- total_occ_map(example_cube_1, level = "country",
                                        region = "Denmark")
plot(to_map)
} # }
if (FALSE) { # \dontrun{
to_ts <- total_occ_ts(example_cube_1, first_year = 1985)
plot(to_ts)
} # }