Fast Quality Checks for Species Occurrence Records
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Documentation for package ‘OccurrenceCleaner’ version 0.2.0
Help Pages
| as_spatialvalid | Convert flags to CoordinateCleaner's spatialvalid format |
| clean_age_equal | Test: fossil age range |
| clean_age_outlier | Test: fossil age outliers |
| clean_age_range_outlier | Test: fossil age-range outliers |
| clean_aohi | Test: artificial hotspots |
| clean_basis_fossil | Tests: basis of record |
| clean_basis_living | Tests: basis of record |
| clean_capital | Test: country capitals |
| clean_centroid | Test: country and province centroids |
| clean_country_mismatch | Test: country code mismatch |
| clean_dataset_ddmm | Test: degree-minute conversion errors in a dataset |
| clean_dataset_rounded | Test: rasterised datasets |
| clean_duplicate | Test: duplicates |
| clean_equal | Test: equal coordinates |
| clean_establishment_introduced | Tests: establishment means |
| clean_establishment_managed | Tests: establishment means |
| clean_gbif_headquarters | Test: GBIF headquarters |
| clean_institution | Test: biodiversity institutions |
| clean_invalid | Test: invalid coordinates |
| clean_issue_coordinate | Tests: GBIF issue flags |
| clean_issue_date | Tests: GBIF issue flags |
| clean_issue_rounded | Tests: GBIF issue flags |
| clean_issue_taxon | Tests: GBIF issue flags |
| clean_land_marine | Tests: habitat at sea and on land |
| clean_outlier | Test: geographic outliers |
| clean_range | Test: outside the species range |
| clean_sea | Test: records at sea |
| clean_sea_nonmarine | Tests: habitat at sea and on land |
| clean_spatiotemporal_outlier | Test: fossil outliers in space and time |
| clean_urban | Test: urban areas |
| clean_zero | Test: zero coordinates |
| download_reference | Download the 1:10 million land layer |
| export_pyrate | Export fossil records as PyRate input |
| flagged_table | Read flag output written by flag_occurrences() |
| flag_mask | Bit mask and membership for sets of tests |
| flag_occurrences | Flag occurrence records |
| flag_reference | Reference data behind a set of flags |
| flag_tests | The flag layout: one bit per test |
| gentiana | GBIF records of gentians in Austria |
| has_flag | Bit mask and membership for sets of tests |
| keep_unflagged | Keep the records no test flagged |
| occ_columns | Name the record fields |
| plot.occ_flagged | Plot flag percentages, or map flagged records |
| plot.occ_flags | Plot flag percentages, or map flagged records |
| plot.occ_summary | Plot flag percentages, or map flagged records |
| plot.occ_tally | Plot flag percentages, or map flagged records |
| read_flagged | Read flag output written by flag_occurrences() |
| reference_habitat | Genus habitats of the habitat tests |
| reference_info | Reference data: sources and versions |
| reference_points | Reference points of a proximity test |
| summary.occ_flagged | Share of records flagged, per test and rule |
| summary.occ_flags | Share of records flagged, per test and rule |
| summary.occ_tally | Share of records flagged, per test and rule |
| tally_flags | Tally flags into a loss table |
| test_age_equal | Test: fossil age range |
| test_age_outlier | Test: fossil age outliers |
| test_age_range_outlier | Test: fossil age-range outliers |
| test_aohi | Test: artificial hotspots |
| test_basis | Tests: basis of record |
| test_capital | Test: country capitals |
| test_centroid | Test: country and province centroids |
| test_country_mismatch | Test: country code mismatch |
| test_dataset_ddmm | Test: degree-minute conversion errors in a dataset |
| test_dataset_rounded | Test: rasterised datasets |
| test_duplicate | Test: duplicates |
| test_equal | Test: equal coordinates |
| test_establishment | Tests: establishment means |
| test_gbif_headquarters | Test: GBIF headquarters |
| test_gbif_issue | Tests: GBIF issue flags |
| test_habitat | Tests: habitat at sea and on land |
| test_institution | Test: biodiversity institutions |
| test_invalid | Test: invalid coordinates |
| test_outlier | Test: geographic outliers |
| test_plan | Which tests run on an input |
| test_range | Test: outside the species range |
| test_sea | Test: records at sea |
| test_spatiotemporal_outlier | Test: fossil outliers in space and time |
| test_urban | Test: urban areas |
| test_zero | Test: zero coordinates |