Test: biodiversity institutions

Flags records within 100 m of a biodiversity institution (WGS84 geodesic distance, closed ball): herbaria, museums, botanic gardens, zoos and universities holding collections, where specimens are often georeferenced to the institution. The default gazetteer contains 23,895 points: the 6,080 institutions with coordinates in GBIF's Global Registry of Scientific Collections (GRSciColl), less five whose coordinates the zero test flags (they lie near (0, 0) or have a longitude of exactly 0, and are geocoding errors); 7,810 points from Wikidata (CC0), retrieved 2026-10-10: every botanical garden, natural history museum, zoo, aquarium and herbarium with coordinates, every museum whose subject is a natural-history field, and the museums of Wikipedia's lists of natural history museums (English, Arabic, Dutch, Esperanto, French, German and Portuguese editions) that have their own Wikidata coordinates; 700 further museums of those lists placed at the place the list gives for them, by its Wikidata coordinates or the GeoNames populated place of that name (source "Wikipedia", master_source says which); the three GeoNames places (CC BY 4.0) of CoordinateCleaner's table; 3,652 gardens of Botanic Gardens Conservation International (BGCI) GardenSearch, retrieved 2026-10-10, used under the BGCI terms (https://www.bgci.org/terms-and-conditions/); 1,062 herbaria of Index Herbariorum that GRSciColl does not place, and 2,468 publishing organisations of the GBIF registry, both retrieved 2026-10-13; and 2,120 points for the institutions of CoordinateCleaner's table that none of these holds under their name (source "CoordinateCleaner list"), placed from Wikidata, OpenStreetMap (through Nominatim) or the GeoNames populated place of the institution's city, by its name, city and country; master_source says which. The source column of reference_points() tells them apart.

Usage

clean_institution(x, buffer = 100, ...)

Arguments

x: A data frame of occurrence records.
buffer: Buffer distance of the test, in the unit of its Buffer section; the default is the test's default buffer.
...: Further arguments to flag_occurrences(): columns, reference, gazetteers, land_scale.

Value

clean_<test>(): the rows of x the test does not flag, with the columns of x unchanged. See keep_unflagged(), Cleaning functions.

Details

Every institution of CoordinateCleaner's table with coordinates has a point here except one, an expert group listed in Antarctica. Where a source gives several candidates for an institution, the one nearest CoordinateCleaner's point is taken; the coordinates are always the source's. For 496 institutions no source places the institution itself, and the point is the populated place of its country nearest CoordinateCleaner's point.

The exception is "SCAR - Expert Group on Birds and Marine Mammals". CoordinateCleaner places it at 45.1439 N, 0.5558 E. Its entry in the GBIF registry was deleted on 2021-05-31 and has no coordinates. It has no point here because no independently verified physical location of the group could be established.

The column extension marks the 7,665 points from sources CoordinateCleaner's table does not draw on: Wikidata beyond the museums of the English list, and the lists of the other language editions. The other 16,230 points come from the registries CoordinateCleaner's table is compiled from (GRSciColl, which absorbed GRBio and mirrors Index Herbariorum, Index Herbariorum itself, the GBIF registry, the English list, GeoNames and BGCI) and from its own list of institutions. Passing the points with extension FALSE as gazetteers = list(institution = ...) restricts the test to those sources (see the examples).

Fields

lon, lat.

Buffer

buffers = list(institution = 100), in metres.

CoordinateCleaner

Equivalent to cc_inst(). Its 40-gon buffer edge lies within 0.31 m of the 100 m circle. Its institutions table (9,773 points with coordinates) places nearly every institution by its own geocoding, so its points can lie apart from the source coordinates used here: for 32 percent of its points a point of the default gazetteer lies within 100 m, for 73 percent within 1 km and for 91 percent within 5 km (28, 70 and 90 percent for the points with extension FALSE). reference = "CoordinateCleaner" uses that table, and rbind() of reference_points() under both references, passed as gazetteers = list(institution = ...), flags records near either.

Custom gazetteer

gazetteers = list(institution = points), a data frame of longitude and latitude; see flag_occurrences().

Examples

x <- data.frame(decimalLongitude = c(16.3598, 15), decimalLatitude = c(48.2052, 47))
flag_occurrences(x, tests = "institution")$flag_institution
g <- reference_points("institution")
flag_occurrences(x, tests = "institution",
                 gazetteers = list(institution = g[!g$extension, ]))$flag_institution
clean_institution(x)