Package index

Flagging

flag_occurrences()

Flag occurrence records

test_plan()

Which tests run on an input

occ_columns()

Name the record fields

Tests

clean_invalid()

Test: invalid coordinates

clean_zero()

Test: zero coordinates

clean_equal()

Test: equal coordinates

clean_capital()

Test: country capitals

clean_centroid()

Test: country and province centroids

clean_institution()

Test: biodiversity institutions

clean_gbif_headquarters()

Test: GBIF headquarters

clean_sea()

Test: records at sea

clean_urban()

Test: urban areas

clean_country_mismatch()

Test: country code mismatch

clean_duplicate()

Test: duplicates

clean_issue_coordinate() clean_issue_taxon() clean_issue_date() clean_issue_rounded()

Tests: GBIF issue flags

clean_basis_fossil() clean_basis_living()

Tests: basis of record

clean_establishment_introduced() clean_establishment_managed()

Tests: establishment means

clean_age_equal()

Test: fossil age range

clean_outlier()

Test: geographic outliers

clean_age_outlier()

Test: fossil age outliers

clean_spatiotemporal_outlier()

Test: fossil outliers in space and time

clean_age_range_outlier()

Test: fossil age-range outliers

clean_dataset_ddmm()

Test: degree-minute conversion errors in a dataset

clean_dataset_rounded()

Test: rasterised datasets

clean_range()

Test: outside the species range

clean_aohi()

Test: artificial hotspots

clean_sea_nonmarine() clean_land_marine()

Tests: habitat at sea and on land

Rules and tallies

keep_unflagged()

Keep the records no test flagged

tally_flags()

Tally flags into a loss table

summary(<occ_flags>) summary(<occ_flagged>) summary(<occ_tally>)

Share of records flagged, per test and rule

plot(<occ_summary>) plot(<occ_tally>) plot(<occ_flags>) plot(<occ_flagged>)

Plot flag percentages, or map flagged records

flag_mask() has_flag()

Bit mask and membership for sets of tests

flag_tests()

The flag layout: one bit per test

On-disk output

read_flagged() flagged_table()

Read flag output written by flag_occurrences()

Export

export_pyrate()

Export fossil records as PyRate input

as_spatialvalid()

Convert flags to CoordinateCleaner's spatialvalid format

Reference data

reference_info()

Reference data: sources and versions

flag_reference()

Reference data behind a set of flags

reference_points()

Reference points of a proximity test

reference_habitat()

Genus habitats of the habitat tests

download_reference()

Download the 1:10 million land layer

Data

gentiana

GBIF records of gentians in Austria

Package

OccurrenceCleaner OccurrenceCleaner-package

OccurrenceCleaner: fast quality flags for species occurrence records