Nothing
tests/testthat/test-PaigeIntegrater.R
In BeeBDC: Occurrence Data Cleaning
requireNamespace("readr")
requireNamespace("BeeBDC")
requireNamespace("dplyr")
## existing data
db_standardized <- dplyr::tribble(
~decimalLatitude, ~decimalLongitude, ~recordNumber, ~recordedBy, ~individualCount, ~samplingProtocol, ~associatedTaxa, ~sex, ~catalogNumber, ~institutionCode, ~otherCatalogNumbers, ~recordId, ~occurrenceID, ~collectionID, ~genus, ~specificEpithet, ~id, ~locality, ~database_id, ~scientificName, ~infraspecificEpithet, ~country, ~coordinateUncertaintyInMeters,
2.233, -90L, NA, "James Ogilvie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323864", "AMNH", NA, NA, "85fb767f-1f99-482f-896c-69dce8b59097", NA, "Pseudoanthidium", "truncatum", NA, NA, "db_fake_1", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323581", "AMNH", NA, NA, "63f56ed1-7391-4814-a298-c1b67ca986be", NA, "Halictus", "simplex", NA, "near Weing Sa", "db_fake_2", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell & Wilmatte P. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323583", "AMNH", NA, NA, "cde3718b-8621-4b3f-b203-4436961a4b73", NA, "Halictus", "simplex", NA, "Lake Waskesiu, at the beginning of the portage to Heart Lakes", "db_fake_3", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "C. S. Brimley", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324010", "AMNH", NA, NA, "82e1eab7-5d92-4358-aede-1fab15ba4eda", NA, "Halictus", "simplex", NA, NA, "db_fake_4", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323630", "AMNH", NA, NA, "c161e78e-c091-4483-adf4-6b54045283d7", NA, "Halictus", "simplex", NA, "Prince Albert National Park, Lake Ajawaan", "db_fake_5", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323584", "AMNH", NA, NA, "002a4861-5374-46ac-84d4-087762ba0c88", NA, "Halictus", "simplex", NA, NA, "db_fake_6", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell & Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323616", "AMNH", NA, NA, "5e848030-8e9d-4f64-873d-08fee631e7dd", NA, "Halictus", "simplex", NA, NA, "db_fake_7", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Alice M. Mackie", 1L, NA, NA, "MALE", "AMNH_IZC 00323619", "AMNH", NA, NA, "250ba041-2727-43d0-a39e-8d3470f5a8bf", NA, "Halictus", "simplex", NA, NA, "db_fake_8", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323591", "AMNH", NA, NA, "4cad3ea9-11b3-4589-b1d1-0035a84ea861", NA, "Halictus", "simplex", NA, NA, "db_fake_9", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323601", "AMNH", NA, NA, "dc3ebe14-f11f-45e9-b121-d34a8693284e", NA, "Halictus", "simplex", NA, NA, "db_fake_10", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "A. H. Manes", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324011", "AMNH", NA, NA, "6f1d8a81-3a4a-4650-be8c-7102f073e90e", NA, "Halictus", "simplex", NA, NA, "db_fake_11", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323627", "AMNH", NA, NA, "406433bc-9c08-4e94-9768-d8df0bdd92cb", NA, "Halictus", "simplex", NA, NA, "db_fake_12", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323611", "AMNH", NA, NA, "bf53740e-e96c-4b5a-a0e9-6b4bea3b2448", NA, "Halictus", "simplex", NA, "Kaieteur National Park", "db_fake_13", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323613", "AMNH", NA, NA, "2e6d4df0-0a46-4837-b340-ed6f8166a831", NA, "Halictus", "simplex", NA, "Kum Puang Creek", "db_fake_14", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Alice M. Mackie", 1L, NA, NA, NA, "AMNH_IZC 00323617", "AMNH", NA, NA, "c0642780-37dc-4625-8a30-eacd5dbd1b70", NA, "Halictus", "simplex", NA, NA, "db_fake_15", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "Fake_data_1", "AMNH", NA, NA, "259d5501-c49c-4a0b-99fc-1595ffe403b1", NA, "Halictus", "simplex", NA, NA, "db_fake_16", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_2", "Bee Place", NA, NA, "not_a_number1", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_17", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_3", "Bee Place", NA, NA, "not_a_number2", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_18", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_4", "Bee Place", NA, NA, "not_a_number3", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_19", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_5", "Bee Place", NA, NA, "not_a_number4", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_20", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_6", "Bee Place", NA, NA, "not_a_number5", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_21", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_7", "Bee Place", NA, NA, "not_a_number6", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_22", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_8", "Bee Place", NA, NA, "not_a_number7", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_23", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_9", "Bee Place", NA, NA, "not_a_number8", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_24", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_10", "Bee Place", NA, NA, "not_a_number9", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_25", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_11", "Bee Place", NA, NA, "not_a_number10", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_26", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_12", "Bee Place", NA, NA, "not_a_number11", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_27", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_13", "Bee Place", NA, NA, "not_a_number12", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_28", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_14", "Bee Place", NA, NA, "not_a_number13", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_29", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_15", "Bee Place", NA, NA, "not_a_number14", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_30", "Fake species", "species", "The incorporated states of nowhere", 100L
)
## Paige corrections - this is FAKED DATA AND SHOULD NOT BE USED FOR ANYTHING EVER OTHER THAN THIS TEST
PaigeNAm <- dplyr::tribble(
~X.1, ~X, ~scientificName, ~id, ~institutionCode, ~collectionCode, ~ownerInstitutionCode, ~collectionID, ~basisOfRecord, ~occurrenceID, ~catalogNumber, ~otherCatalogNumbers, ~kingdom, ~phylum, ~class, ~order, ~family, ~taxonID, ~scientificNameAuthorship, ~genus, ~specificEpithet, ~taxonRank, ~infraspecificEpithet, ~identifiedBy, ~dateIdentified, ~identificationReferences, ~identificationRemarks, ~taxonRemarks, ~identificationQualifier, ~typeStatus, ~recordedBy, ~recordNumber, ~eventDate, ~year, ~month, ~day, ~startDayOfYear, ~endDayOfYear, ~verbatimEventDate, ~occurrenceRemarks, ~habitat, ~fieldNumber, ~informationWithheld, ~dataGeneralizations, ~dynamicProperties, ~associatedTaxa, ~associatedOccurrences, ~reproductiveCondition, ~establishmentMeans, ~lifeStage, ~sex, ~individualCount, ~samplingProtocol, ~samplingEffort, ~preparations, ~country, ~stateProvince, ~county, ~municipality, ~locality, ~locationRemarks, ~decimalLatitude, ~decimalLongitude, ~geodeticDatum, ~coordinateUncertaintyInMeters, ~verbatimCoordinates, ~georeferencedBy, ~georeferenceProtocol, ~georeferenceSources, ~georeferenceVerificationStatus, ~georeferenceRemarks, ~minimumElevationInMeters, ~maximumElevationInMeters, ~minimumDepthInMeters, ~maximumDepthInMeters, ~verbatimDepth, ~verbatimElevation, ~disposition, ~language, ~recordEnteredBy, ~modified, ~rights, ~rightsHolder, ~accessRights, ~recordId, ~references, ~finalLatitude, ~finalLongitude, ~Identifier_Level, ~PrecisionLevel, ~Source, ~geolocate_LocalityID, ~geolocate_ResultID, ~geolocate_Latitude, ~geolocate_Longitude, ~geolocate_UncertaintyRadiusMeters, ~geolocate_UncertaintyPolygon, ~geolocate_Score, ~geolocate_Precision, ~geolocate_ParsePattern, ~geolocate_locFieldUsed, ~geolocate_NumResults, ~wordCount, ~finalName, ~CountryName,
1L, 20102L, "Agapostemon borealis", 1317390166L, "USNM", "Entomology", NA, NA, "PRESERVED_SPECIMEN", "http://n2t.net/ark:/65665/3084be498-793e-4b29-bb1d-0ad85253ef61", NA, NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "borealis", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "Livingston", NA, "1896-04-04T00:00:00Z", 1896L, "4", 4L, 95L, NA, "4/4/1996", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "FEMALE", 1L, NA, NA, "Pinned", "CA", "British Columbia", NA, NA, "Vancouver", NA, 2.233, -90, NA, 10206L, NA, NA, "GEOLocate", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 49.25, -123.133, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon texanus", "Canada",
2L, 20103L, "Agapostemon californicus", 1101319745L, "UCM", "UCMC", NA, NA, "PRESERVED_SPECIMEN", "7f6a4b80-642d-40f2-8dc7-eb45235f157c", NA, NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "californicus", "SPECIES", NA, "T.D.A. Cockerell", "1939-01-01T00:00:00Z", NA, NA, NA, NA, NA, "T.D.A. Cockerell", NA, NA, NA, "Jun. 18", NA, NA, NA, "Jun. 18", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pinned", "US", "California", "Los Angeles County", NA, "San Clemente Island", NA, 2.233, -90, NA, 21236L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-06-29T00:00:00Z", NA, NA, NA, NA, NA, 32.9, -118.5009, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon texanus", "United States",
5L, 23836L, "Agapostemon leunculus", 658242510L, "KU", "SEMC", NA, NA, "PRESERVED_SPECIMEN", "3aa3dd4b-1ed6-11e3-bfac-90b11c41863e", "495676", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Roberts, R", NA, NA, NA, NA, NA, NA, "Univ. of Kans. Mex. Exped.", NA, "1961-06-11T00:00:00Z", 1961L, "6", 11L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, NA, NA, NA, "Pinned - 1", "MX", "Veracruz", NA, NA, "Alazan, 7 mi NW nr Tuxpan", NA, 20.9915, -97.54551, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 20.9915, -97.54551, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
6L, 23837L, "Agapostemon leunculus", 1060982746L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511822", "EMEC511822", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-06-29T00:00:00Z", 1962L, "6", 29L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Sinaloa", NA, NA, "Rosario", NA, 22.99325, -105.8586, NA, 1405L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-06-24T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511822&one=T", 22.99325, -105.8586, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
7L, 23838L, "Agapostemon leunculus", 219014691L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", "not_a_number1", "300182", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Alicia Rodríguez Palafox", NA, "1993-04-23T00:00:00Z", 1993L, "4", 23L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Ocosingo, Ej. Shanil, 52.9 km N", NA, 17.21667, -92.1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 17.21667, -92.1, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
8L, 23839L, "Agapostemon leunculus", 1060924636L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511782", "EMEC511782", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-27T00:00:00Z", 1962L, "7", 27L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 17.06371, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511782&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
9L, 23840L, "Agapostemon leunculus", 1060924589L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511766", "EMEC511766", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-27T00:00:00Z", 1962L, "7", 27L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 2.233, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511766&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
10L, 23841L, "Agapostemon leunculus", 219014682L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", "not_a_number11", "300173", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "J. L. Neff", NA, "1993-04-12T00:00:00Z", 1993L, "4", 12L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Tuxtla Gutierrez, 37 km E", NA, 2.233, 90, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.75, -92.91667, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
11L, 23842L, "Agapostemon leunculus", 219014681L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", NA, "300172", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Wallace E. LaBerge", NA, "1993-04-10T00:00:00Z", 1993L, "4", 10L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Ocozocoautla, 17 km N", NA, 16.89, -93.46, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.89, -93.46, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
12L, 23843L, "Agapostemon leunculus", 657759380L, "KU", "SEMC", NA, NA, "PRESERVED_SPECIMEN", "1fc6766a-1ed6-11e3-bfac-90b11c41863e", "496619", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Roberts, R", NA, NA, NA, NA, NA, NA, "Univ. of Kans. Mex. Exped.", NA, "1954-08-22T00:00:00Z", 1954L, "8", 22L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, NA, NA, NA, "Pinned - 1", "MX", "San Luis Potosi", NA, NA, "Ciudad Maiz, 5 mi E", NA, 22.44681, -99.56705, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 22.44681, -99.56705, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
13L, 23844L, "Agapostemon leunculus", 1060924663L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511764", "EMEC511764", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-27T00:00:00Z", 1962L, "7", 27L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 17.06371, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511764&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
14L, 23845L, "Agapostemon leunculus", 657733166L, "KU", "SEMC", NA, NA, "PRESERVED_SPECIMEN", "1e5ca92c-1ed6-11e3-bfac-90b11c41863e", "495671", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Roberts, R", NA, NA, NA, NA, NA, NA, "Univ. of Kans. Mex. Exped.", NA, "1961-06-11T00:00:00Z", 1961L, "6", 11L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, NA, NA, NA, "Pinned - 1", "MX", "Veracruz", NA, NA, "Alazan, 7 mi NW nr Tuxpan", NA, 20.9915, -97.54551, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 20.9915, -97.54551, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
15L, 23846L, "Agapostemon leunculus", 1060924629L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511794", "EMEC511794", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-26T00:00:00Z", 1962L, "7", 26L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 17.06371, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511794&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
16L, 23847L, "Agapostemon leunculus", 219014679L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", NA, "300170", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Felipe Noguera Martínez", NA, "1993-04-10T00:00:00Z", 1993L, "4", 10L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Ocozocoautla, 17 km N", NA, 16.89, -93.46, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.89, -93.46, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
17L, 23848L, "Agapostemon leunculus", 219014687L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", NA, "300178", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Claudia Mendoza", NA, "1993-04-13T00:00:00Z", 1993L, "4", 13L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Teopisca", NA, 16.53333, -92.46667, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.53333, -92.46667, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico"
) %>%
# Change the column name from Source to dataSource to match the rest of the data.
dplyr::rename(dataSource = Source) %>%
# EXTRACT WAS HERE
# add a NEW database_id column
dplyr::mutate(
database_id = paste0("Paige_data_", 1:nrow(.)),
.before = scientificName)
columnList <- list(c("decimalLatitude", "decimalLongitude",
"recordNumber", "recordedBy", "individualCount", "samplingProtocol",
"associatedTaxa", "sex", "catalogNumber", "institutionCode", "otherCatalogNumbers",
"recordId", "occurrenceID", "collectionID"), # Iteration 1
c("catalogNumber", "institutionCode", "otherCatalogNumbers",
"recordId", "occurrenceID", "collectionID"), # Iteration 2
c("decimalLatitude", "decimalLongitude",
"recordedBy", "genus", "specificEpithet"), # Iteration 3
c("id", "decimalLatitude", "decimalLongitude"), # Iteration 4
c("recordedBy", "genus", "specificEpithet", "locality"), # Iteration 5
c("recordedBy", "institutionCode", "genus",
"specificEpithet","locality"),# Iteration 6
c("occurrenceID","decimalLatitude", "decimalLongitude"), # Iteration 7
c("catalogNumber","decimalLatitude", "decimalLongitude"), # Iteration 8
c("catalogNumber", "locality") # Iteration 9
)
## generate new data using function
testOut <- BeeBDC::PaigeIntegrater(db_standardized = db_standardized,
PaigeNAm = PaigeNAm,
columnStrings = columnList)
## test the function
# the correct answer
correct <- dplyr::tribble(
~decimalLatitude, ~decimalLongitude, ~recordNumber, ~recordedBy, ~individualCount, ~samplingProtocol, ~associatedTaxa, ~sex, ~catalogNumber, ~institutionCode, ~otherCatalogNumbers, ~recordId, ~occurrenceID, ~collectionID, ~genus, ~specificEpithet, ~id, ~locality, ~database_id, ~scientificName, ~infraspecificEpithet, ~country, ~coordinateUncertaintyInMeters,
2.233, -90, NA, "James Ogilvie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323864", "AMNH", NA, NA, "85fb767f-1f99-482f-896c-69dce8b59097", NA, "Pseudoanthidium", "truncatum", NA, NA, "db_fake_1", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323581", "AMNH", NA, NA, "63f56ed1-7391-4814-a298-c1b67ca986be", NA, "Halictus", "simplex", NA, "near Weing Sa", "db_fake_2", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell & Wilmatte P. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323583", "AMNH", NA, NA, "cde3718b-8621-4b3f-b203-4436961a4b73", NA, "Halictus", "simplex", NA, "Lake Waskesiu, at the beginning of the portage to Heart Lakes", "db_fake_3", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "C. S. Brimley", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324010", "AMNH", NA, NA, "82e1eab7-5d92-4358-aede-1fab15ba4eda", NA, "Halictus", "simplex", NA, NA, "db_fake_4", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323630", "AMNH", NA, NA, "c161e78e-c091-4483-adf4-6b54045283d7", NA, "Halictus", "simplex", NA, "Prince Albert National Park, Lake Ajawaan", "db_fake_5", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323584", "AMNH", NA, NA, "002a4861-5374-46ac-84d4-087762ba0c88", NA, "Halictus", "simplex", NA, NA, "db_fake_6", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell & Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323616", "AMNH", NA, NA, "5e848030-8e9d-4f64-873d-08fee631e7dd", NA, "Halictus", "simplex", NA, NA, "db_fake_7", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Alice M. Mackie", 1L, NA, NA, "MALE", "AMNH_IZC 00323619", "AMNH", NA, NA, "250ba041-2727-43d0-a39e-8d3470f5a8bf", NA, "Halictus", "simplex", NA, NA, "db_fake_8", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323591", "AMNH", NA, NA, "4cad3ea9-11b3-4589-b1d1-0035a84ea861", NA, "Halictus", "simplex", NA, NA, "db_fake_9", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323601", "AMNH", NA, NA, "dc3ebe14-f11f-45e9-b121-d34a8693284e", NA, "Halictus", "simplex", NA, NA, "db_fake_10", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "A. H. Manes", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324011", "AMNH", NA, NA, "6f1d8a81-3a4a-4650-be8c-7102f073e90e", NA, "Halictus", "simplex", NA, NA, "db_fake_11", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323627", "AMNH", NA, NA, "406433bc-9c08-4e94-9768-d8df0bdd92cb", NA, "Halictus", "simplex", NA, NA, "db_fake_12", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323611", "AMNH", NA, NA, "bf53740e-e96c-4b5a-a0e9-6b4bea3b2448", NA, "Halictus", "simplex", NA, "Kaieteur National Park", "db_fake_13", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323613", "AMNH", NA, NA, "2e6d4df0-0a46-4837-b340-ed6f8166a831", NA, "Halictus", "simplex", NA, "Kum Puang Creek", "db_fake_14", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Alice M. Mackie", 1L, NA, NA, NA, "AMNH_IZC 00323617", "AMNH", NA, NA, "c0642780-37dc-4625-8a30-eacd5dbd1b70", NA, "Halictus", "simplex", NA, NA, "db_fake_15", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "Fake_data_1", "AMNH", NA, NA, "259d5501-c49c-4a0b-99fc-1595ffe403b1", NA, "Halictus", "simplex", NA, NA, "db_fake_16", "Fake species", "species", "The incorporated states of nowhere", 100L,
17.21667, -92.1, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_2", "Bee Place", NA, NA, "not_a_number1", NA, "Agapostemon", "leunculus", NA, "non-existent", "Paige_data_5", "Agapostemon leunculus", "species", "MX", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_3", "Bee Place", NA, NA, "not_a_number2", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_18", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_4", "Bee Place", NA, NA, "not_a_number3", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_19", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_5", "Bee Place", NA, NA, "not_a_number4", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_20", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_6", "Bee Place", NA, NA, "not_a_number5", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_21", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_7", "Bee Place", NA, NA, "not_a_number6", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_22", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_8", "Bee Place", NA, NA, "not_a_number7", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_23", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_9", "Bee Place", NA, NA, "not_a_number8", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_24", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_10", "Bee Place", NA, NA, "not_a_number9", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_25", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_11", "Bee Place", NA, NA, "not_a_number10", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_26", "Fake species", "species", "The incorporated states of nowhere", 100L,
16.75, -92.91667, NA, "Nope", NA, NA, NA, NA, "Fake_data_12", "Bee Place", NA, NA, "not_a_number11", NA, "Agapostemon", "leunculus", NA, "non-existent", "Paige_data_8", "Agapostemon leunculus", "species", "MX", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_13", "Bee Place", NA, NA, "not_a_number12", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_28", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_14", "Bee Place", NA, NA, "not_a_number13", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_29", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_15", "Bee Place", NA, NA, "not_a_number14", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_30", "Fake species", "species", "The incorporated states of nowhere", 100L
)
testthat::test_that("PaigeIntegrater revised datatable with correct values", {
testthat::expect_equal(testOut, correct)
})
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requireNamespace("readr")
requireNamespace("BeeBDC")
requireNamespace("dplyr")
## existing data
db_standardized <- dplyr::tribble(
~decimalLatitude, ~decimalLongitude, ~recordNumber, ~recordedBy, ~individualCount, ~samplingProtocol, ~associatedTaxa, ~sex, ~catalogNumber, ~institutionCode, ~otherCatalogNumbers, ~recordId, ~occurrenceID, ~collectionID, ~genus, ~specificEpithet, ~id, ~locality, ~database_id, ~scientificName, ~infraspecificEpithet, ~country, ~coordinateUncertaintyInMeters,
2.233, -90L, NA, "James Ogilvie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323864", "AMNH", NA, NA, "85fb767f-1f99-482f-896c-69dce8b59097", NA, "Pseudoanthidium", "truncatum", NA, NA, "db_fake_1", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323581", "AMNH", NA, NA, "63f56ed1-7391-4814-a298-c1b67ca986be", NA, "Halictus", "simplex", NA, "near Weing Sa", "db_fake_2", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell & Wilmatte P. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323583", "AMNH", NA, NA, "cde3718b-8621-4b3f-b203-4436961a4b73", NA, "Halictus", "simplex", NA, "Lake Waskesiu, at the beginning of the portage to Heart Lakes", "db_fake_3", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "C. S. Brimley", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324010", "AMNH", NA, NA, "82e1eab7-5d92-4358-aede-1fab15ba4eda", NA, "Halictus", "simplex", NA, NA, "db_fake_4", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323630", "AMNH", NA, NA, "c161e78e-c091-4483-adf4-6b54045283d7", NA, "Halictus", "simplex", NA, "Prince Albert National Park, Lake Ajawaan", "db_fake_5", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323584", "AMNH", NA, NA, "002a4861-5374-46ac-84d4-087762ba0c88", NA, "Halictus", "simplex", NA, NA, "db_fake_6", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell & Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323616", "AMNH", NA, NA, "5e848030-8e9d-4f64-873d-08fee631e7dd", NA, "Halictus", "simplex", NA, NA, "db_fake_7", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Alice M. Mackie", 1L, NA, NA, "MALE", "AMNH_IZC 00323619", "AMNH", NA, NA, "250ba041-2727-43d0-a39e-8d3470f5a8bf", NA, "Halictus", "simplex", NA, NA, "db_fake_8", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323591", "AMNH", NA, NA, "4cad3ea9-11b3-4589-b1d1-0035a84ea861", NA, "Halictus", "simplex", NA, NA, "db_fake_9", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323601", "AMNH", NA, NA, "dc3ebe14-f11f-45e9-b121-d34a8693284e", NA, "Halictus", "simplex", NA, NA, "db_fake_10", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "A. H. Manes", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324011", "AMNH", NA, NA, "6f1d8a81-3a4a-4650-be8c-7102f073e90e", NA, "Halictus", "simplex", NA, NA, "db_fake_11", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323627", "AMNH", NA, NA, "406433bc-9c08-4e94-9768-d8df0bdd92cb", NA, "Halictus", "simplex", NA, NA, "db_fake_12", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323611", "AMNH", NA, NA, "bf53740e-e96c-4b5a-a0e9-6b4bea3b2448", NA, "Halictus", "simplex", NA, "Kaieteur National Park", "db_fake_13", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323613", "AMNH", NA, NA, "2e6d4df0-0a46-4837-b340-ed6f8166a831", NA, "Halictus", "simplex", NA, "Kum Puang Creek", "db_fake_14", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Alice M. Mackie", 1L, NA, NA, NA, "AMNH_IZC 00323617", "AMNH", NA, NA, "c0642780-37dc-4625-8a30-eacd5dbd1b70", NA, "Halictus", "simplex", NA, NA, "db_fake_15", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "Fake_data_1", "AMNH", NA, NA, "259d5501-c49c-4a0b-99fc-1595ffe403b1", NA, "Halictus", "simplex", NA, NA, "db_fake_16", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_2", "Bee Place", NA, NA, "not_a_number1", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_17", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_3", "Bee Place", NA, NA, "not_a_number2", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_18", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_4", "Bee Place", NA, NA, "not_a_number3", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_19", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_5", "Bee Place", NA, NA, "not_a_number4", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_20", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_6", "Bee Place", NA, NA, "not_a_number5", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_21", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_7", "Bee Place", NA, NA, "not_a_number6", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_22", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_8", "Bee Place", NA, NA, "not_a_number7", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_23", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_9", "Bee Place", NA, NA, "not_a_number8", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_24", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_10", "Bee Place", NA, NA, "not_a_number9", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_25", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_11", "Bee Place", NA, NA, "not_a_number10", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_26", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_12", "Bee Place", NA, NA, "not_a_number11", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_27", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_13", "Bee Place", NA, NA, "not_a_number12", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_28", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_14", "Bee Place", NA, NA, "not_a_number13", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_29", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90L, NA, "Nope", NA, NA, NA, NA, "Fake_data_15", "Bee Place", NA, NA, "not_a_number14", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_30", "Fake species", "species", "The incorporated states of nowhere", 100L
)
## Paige corrections - this is FAKED DATA AND SHOULD NOT BE USED FOR ANYTHING EVER OTHER THAN THIS TEST
PaigeNAm <- dplyr::tribble(
~X.1, ~X, ~scientificName, ~id, ~institutionCode, ~collectionCode, ~ownerInstitutionCode, ~collectionID, ~basisOfRecord, ~occurrenceID, ~catalogNumber, ~otherCatalogNumbers, ~kingdom, ~phylum, ~class, ~order, ~family, ~taxonID, ~scientificNameAuthorship, ~genus, ~specificEpithet, ~taxonRank, ~infraspecificEpithet, ~identifiedBy, ~dateIdentified, ~identificationReferences, ~identificationRemarks, ~taxonRemarks, ~identificationQualifier, ~typeStatus, ~recordedBy, ~recordNumber, ~eventDate, ~year, ~month, ~day, ~startDayOfYear, ~endDayOfYear, ~verbatimEventDate, ~occurrenceRemarks, ~habitat, ~fieldNumber, ~informationWithheld, ~dataGeneralizations, ~dynamicProperties, ~associatedTaxa, ~associatedOccurrences, ~reproductiveCondition, ~establishmentMeans, ~lifeStage, ~sex, ~individualCount, ~samplingProtocol, ~samplingEffort, ~preparations, ~country, ~stateProvince, ~county, ~municipality, ~locality, ~locationRemarks, ~decimalLatitude, ~decimalLongitude, ~geodeticDatum, ~coordinateUncertaintyInMeters, ~verbatimCoordinates, ~georeferencedBy, ~georeferenceProtocol, ~georeferenceSources, ~georeferenceVerificationStatus, ~georeferenceRemarks, ~minimumElevationInMeters, ~maximumElevationInMeters, ~minimumDepthInMeters, ~maximumDepthInMeters, ~verbatimDepth, ~verbatimElevation, ~disposition, ~language, ~recordEnteredBy, ~modified, ~rights, ~rightsHolder, ~accessRights, ~recordId, ~references, ~finalLatitude, ~finalLongitude, ~Identifier_Level, ~PrecisionLevel, ~Source, ~geolocate_LocalityID, ~geolocate_ResultID, ~geolocate_Latitude, ~geolocate_Longitude, ~geolocate_UncertaintyRadiusMeters, ~geolocate_UncertaintyPolygon, ~geolocate_Score, ~geolocate_Precision, ~geolocate_ParsePattern, ~geolocate_locFieldUsed, ~geolocate_NumResults, ~wordCount, ~finalName, ~CountryName,
1L, 20102L, "Agapostemon borealis", 1317390166L, "USNM", "Entomology", NA, NA, "PRESERVED_SPECIMEN", "http://n2t.net/ark:/65665/3084be498-793e-4b29-bb1d-0ad85253ef61", NA, NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "borealis", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "Livingston", NA, "1896-04-04T00:00:00Z", 1896L, "4", 4L, 95L, NA, "4/4/1996", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "FEMALE", 1L, NA, NA, "Pinned", "CA", "British Columbia", NA, NA, "Vancouver", NA, 2.233, -90, NA, 10206L, NA, NA, "GEOLocate", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 49.25, -123.133, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon texanus", "Canada",
2L, 20103L, "Agapostemon californicus", 1101319745L, "UCM", "UCMC", NA, NA, "PRESERVED_SPECIMEN", "7f6a4b80-642d-40f2-8dc7-eb45235f157c", NA, NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "californicus", "SPECIES", NA, "T.D.A. Cockerell", "1939-01-01T00:00:00Z", NA, NA, NA, NA, NA, "T.D.A. Cockerell", NA, NA, NA, "Jun. 18", NA, NA, NA, "Jun. 18", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pinned", "US", "California", "Los Angeles County", NA, "San Clemente Island", NA, 2.233, -90, NA, 21236L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-06-29T00:00:00Z", NA, NA, NA, NA, NA, 32.9, -118.5009, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon texanus", "United States",
5L, 23836L, "Agapostemon leunculus", 658242510L, "KU", "SEMC", NA, NA, "PRESERVED_SPECIMEN", "3aa3dd4b-1ed6-11e3-bfac-90b11c41863e", "495676", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Roberts, R", NA, NA, NA, NA, NA, NA, "Univ. of Kans. Mex. Exped.", NA, "1961-06-11T00:00:00Z", 1961L, "6", 11L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, NA, NA, NA, "Pinned - 1", "MX", "Veracruz", NA, NA, "Alazan, 7 mi NW nr Tuxpan", NA, 20.9915, -97.54551, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 20.9915, -97.54551, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
6L, 23837L, "Agapostemon leunculus", 1060982746L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511822", "EMEC511822", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-06-29T00:00:00Z", 1962L, "6", 29L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Sinaloa", NA, NA, "Rosario", NA, 22.99325, -105.8586, NA, 1405L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-06-24T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511822&one=T", 22.99325, -105.8586, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
7L, 23838L, "Agapostemon leunculus", 219014691L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", "not_a_number1", "300182", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Alicia Rodríguez Palafox", NA, "1993-04-23T00:00:00Z", 1993L, "4", 23L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Ocosingo, Ej. Shanil, 52.9 km N", NA, 17.21667, -92.1, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 17.21667, -92.1, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
8L, 23839L, "Agapostemon leunculus", 1060924636L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511782", "EMEC511782", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-27T00:00:00Z", 1962L, "7", 27L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 17.06371, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511782&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
9L, 23840L, "Agapostemon leunculus", 1060924589L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511766", "EMEC511766", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-27T00:00:00Z", 1962L, "7", 27L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 2.233, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511766&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
10L, 23841L, "Agapostemon leunculus", 219014682L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", "not_a_number11", "300173", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "J. L. Neff", NA, "1993-04-12T00:00:00Z", 1993L, "4", 12L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Tuxtla Gutierrez, 37 km E", NA, 2.233, 90, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.75, -92.91667, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
11L, 23842L, "Agapostemon leunculus", 219014681L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", NA, "300172", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Wallace E. LaBerge", NA, "1993-04-10T00:00:00Z", 1993L, "4", 10L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Ocozocoautla, 17 km N", NA, 16.89, -93.46, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.89, -93.46, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
12L, 23843L, "Agapostemon leunculus", 657759380L, "KU", "SEMC", NA, NA, "PRESERVED_SPECIMEN", "1fc6766a-1ed6-11e3-bfac-90b11c41863e", "496619", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Roberts, R", NA, NA, NA, NA, NA, NA, "Univ. of Kans. Mex. Exped.", NA, "1954-08-22T00:00:00Z", 1954L, "8", 22L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, NA, NA, NA, "Pinned - 1", "MX", "San Luis Potosi", NA, NA, "Ciudad Maiz, 5 mi E", NA, 22.44681, -99.56705, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 22.44681, -99.56705, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
13L, 23844L, "Agapostemon leunculus", 1060924663L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511764", "EMEC511764", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-27T00:00:00Z", 1962L, "7", 27L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 17.06371, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511764&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
14L, 23845L, "Agapostemon leunculus", 657733166L, "KU", "SEMC", NA, NA, "PRESERVED_SPECIMEN", "1e5ca92c-1ed6-11e3-bfac-90b11c41863e", "495671", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Roberts, R", NA, NA, NA, NA, NA, NA, "Univ. of Kans. Mex. Exped.", NA, "1961-06-11T00:00:00Z", 1961L, "6", 11L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, NA, NA, NA, "Pinned - 1", "MX", "Veracruz", NA, NA, "Alazan, 7 mi NW nr Tuxpan", NA, 20.9915, -97.54551, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 20.9915, -97.54551, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
15L, 23846L, "Agapostemon leunculus", 1060924629L, "EMEC", "EMEC", NA, NA, "PRESERVED_SPECIMEN", "urn:catalog:EMEC:EMEC:511794", "EMEC511794", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, NA, NA, NA, NA, NA, NA, NA, "A. E. Michelbacher, M. M. Michelbacher", NA, "1962-07-26T00:00:00Z", 1962L, "7", 26L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Adult", NA, 1L, NA, NA, "pin", "MX", "Oaxaca", NA, NA, "Oaxaca", NA, 17.06371, -96.73192, NA, 8339L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "2017-05-04T00:00:00Z", NA, NA, NA, NA, "http://essigdb.berkeley.edu/cgi/eme_query?bnhm_id=EMEC511794&one=T", 17.06371, -96.73192, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
16L, 23847L, "Agapostemon leunculus", 219014679L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", NA, "300170", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Felipe Noguera Martínez", NA, "1993-04-10T00:00:00Z", 1993L, "4", 10L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Ocozocoautla, 17 km N", NA, 16.89, -93.46, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.89, -93.46, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico",
17L, 23848L, "Agapostemon leunculus", 219014687L, "IBUNAM", "EBCC", NA, NA, "UNKNOWN", NA, "300178", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "Halictidae", NA, NA, "Agapostemon", "leunculus", "SPECIES", NA, "Douglas Yanega", NA, NA, NA, NA, NA, NA, "Claudia Mendoza", NA, "1993-04-13T00:00:00Z", 1993L, "4", 13L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "MX", "Chiapas", NA, NA, "Teopisca", NA, 16.53333, -92.46667, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 16.53333, -92.46667, "Specimen", "High", "GBIF", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2L, "Agapostemon leunculus", "Mexico"
) %>%
# Change the column name from Source to dataSource to match the rest of the data.
dplyr::rename(dataSource = Source) %>%
# EXTRACT WAS HERE
# add a NEW database_id column
dplyr::mutate(
database_id = paste0("Paige_data_", 1:nrow(.)),
.before = scientificName)
columnList <- list(c("decimalLatitude", "decimalLongitude",
"recordNumber", "recordedBy", "individualCount", "samplingProtocol",
"associatedTaxa", "sex", "catalogNumber", "institutionCode", "otherCatalogNumbers",
"recordId", "occurrenceID", "collectionID"), # Iteration 1
c("catalogNumber", "institutionCode", "otherCatalogNumbers",
"recordId", "occurrenceID", "collectionID"), # Iteration 2
c("decimalLatitude", "decimalLongitude",
"recordedBy", "genus", "specificEpithet"), # Iteration 3
c("id", "decimalLatitude", "decimalLongitude"), # Iteration 4
c("recordedBy", "genus", "specificEpithet", "locality"), # Iteration 5
c("recordedBy", "institutionCode", "genus",
"specificEpithet","locality"),# Iteration 6
c("occurrenceID","decimalLatitude", "decimalLongitude"), # Iteration 7
c("catalogNumber","decimalLatitude", "decimalLongitude"), # Iteration 8
c("catalogNumber", "locality") # Iteration 9
)
## generate new data using function
testOut <- BeeBDC::PaigeIntegrater(db_standardized = db_standardized,
PaigeNAm = PaigeNAm,
columnStrings = columnList)
## test the function
# the correct answer
correct <- dplyr::tribble(
~decimalLatitude, ~decimalLongitude, ~recordNumber, ~recordedBy, ~individualCount, ~samplingProtocol, ~associatedTaxa, ~sex, ~catalogNumber, ~institutionCode, ~otherCatalogNumbers, ~recordId, ~occurrenceID, ~collectionID, ~genus, ~specificEpithet, ~id, ~locality, ~database_id, ~scientificName, ~infraspecificEpithet, ~country, ~coordinateUncertaintyInMeters,
2.233, -90, NA, "James Ogilvie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323864", "AMNH", NA, NA, "85fb767f-1f99-482f-896c-69dce8b59097", NA, "Pseudoanthidium", "truncatum", NA, NA, "db_fake_1", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323581", "AMNH", NA, NA, "63f56ed1-7391-4814-a298-c1b67ca986be", NA, "Halictus", "simplex", NA, "near Weing Sa", "db_fake_2", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell & Wilmatte P. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323583", "AMNH", NA, NA, "cde3718b-8621-4b3f-b203-4436961a4b73", NA, "Halictus", "simplex", NA, "Lake Waskesiu, at the beginning of the portage to Heart Lakes", "db_fake_3", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "C. S. Brimley", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324010", "AMNH", NA, NA, "82e1eab7-5d92-4358-aede-1fab15ba4eda", NA, "Halictus", "simplex", NA, NA, "db_fake_4", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323630", "AMNH", NA, NA, "c161e78e-c091-4483-adf4-6b54045283d7", NA, "Halictus", "simplex", NA, "Prince Albert National Park, Lake Ajawaan", "db_fake_5", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323584", "AMNH", NA, NA, "002a4861-5374-46ac-84d4-087762ba0c88", NA, "Halictus", "simplex", NA, NA, "db_fake_6", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell & Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323616", "AMNH", NA, NA, "5e848030-8e9d-4f64-873d-08fee631e7dd", NA, "Halictus", "simplex", NA, NA, "db_fake_7", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Alice M. Mackie", 1L, NA, NA, "MALE", "AMNH_IZC 00323619", "AMNH", NA, NA, "250ba041-2727-43d0-a39e-8d3470f5a8bf", NA, "Halictus", "simplex", NA, NA, "db_fake_8", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323591", "AMNH", NA, NA, "4cad3ea9-11b3-4589-b1d1-0035a84ea861", NA, "Halictus", "simplex", NA, NA, "db_fake_9", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "MALE", "AMNH_IZC 00323601", "AMNH", NA, NA, "dc3ebe14-f11f-45e9-b121-d34a8693284e", NA, "Halictus", "simplex", NA, NA, "db_fake_10", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "A. H. Manes", 1L, NA, NA, "FEMALE", "AMNH_IZC 00324011", "AMNH", NA, NA, "6f1d8a81-3a4a-4650-be8c-7102f073e90e", NA, "Halictus", "simplex", NA, NA, "db_fake_11", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323627", "AMNH", NA, NA, "406433bc-9c08-4e94-9768-d8df0bdd92cb", NA, "Halictus", "simplex", NA, NA, "db_fake_12", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Alice M. Mackie", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323611", "AMNH", NA, NA, "bf53740e-e96c-4b5a-a0e9-6b4bea3b2448", NA, "Halictus", "simplex", NA, "Kaieteur National Park", "db_fake_13", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "AMNH_IZC 00323613", "AMNH", NA, NA, "2e6d4df0-0a46-4837-b340-ed6f8166a831", NA, "Halictus", "simplex", NA, "Kum Puang Creek", "db_fake_14", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Alice M. Mackie", 1L, NA, NA, NA, "AMNH_IZC 00323617", "AMNH", NA, NA, "c0642780-37dc-4625-8a30-eacd5dbd1b70", NA, "Halictus", "simplex", NA, NA, "db_fake_15", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "T. D. A. Cockerell", 1L, NA, NA, "FEMALE", "Fake_data_1", "AMNH", NA, NA, "259d5501-c49c-4a0b-99fc-1595ffe403b1", NA, "Halictus", "simplex", NA, NA, "db_fake_16", "Fake species", "species", "The incorporated states of nowhere", 100L,
17.21667, -92.1, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_2", "Bee Place", NA, NA, "not_a_number1", NA, "Agapostemon", "leunculus", NA, "non-existent", "Paige_data_5", "Agapostemon leunculus", "species", "MX", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_3", "Bee Place", NA, NA, "not_a_number2", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_18", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_4", "Bee Place", NA, NA, "not_a_number3", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_19", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_5", "Bee Place", NA, NA, "not_a_number4", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_20", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_6", "Bee Place", NA, NA, "not_a_number5", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_21", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_7", "Bee Place", NA, NA, "not_a_number6", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_22", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_8", "Bee Place", NA, NA, "not_a_number7", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_23", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_9", "Bee Place", NA, NA, "not_a_number8", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_24", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Easter Egg", NA, NA, NA, NA, "Fake_data_10", "Bee Place", NA, NA, "not_a_number9", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_25", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_11", "Bee Place", NA, NA, "not_a_number10", NA, "Augochloropsis", "fulgida", NA, "non-existent", "db_fake_26", "Fake species", "species", "The incorporated states of nowhere", 100L,
16.75, -92.91667, NA, "Nope", NA, NA, NA, NA, "Fake_data_12", "Bee Place", NA, NA, "not_a_number11", NA, "Agapostemon", "leunculus", NA, "non-existent", "Paige_data_8", "Agapostemon leunculus", "species", "MX", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_13", "Bee Place", NA, NA, "not_a_number12", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_28", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_14", "Bee Place", NA, NA, "not_a_number13", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_29", "Fake species", "species", "The incorporated states of nowhere", 100L,
2.233, -90, NA, "Nope", NA, NA, NA, NA, "Fake_data_15", "Bee Place", NA, NA, "not_a_number14", NA, "Lasioglossum", "semicaeruleum", NA, "non-existent", "db_fake_30", "Fake species", "species", "The incorporated states of nowhere", 100L
)
testthat::test_that("PaigeIntegrater revised datatable with correct values", {
testthat::expect_equal(testOut, correct)
})
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