Nothing
tests/testthat/test-repoFinder.R
In BeeBDC: Occurrence Data Cleaning
requireNamespace("readr")
requireNamespace("BeeBDC")
# make some data files for repoFinder to search and save the files
## ALA data
ALA_data <- dplyr::tribble(
~scientificName, ~family, ~subfamily, ~genus, ~subgenus, ~subspecies, ~species, ~specificEpithet, ~infraspecificEpithet, ~acceptedNameUsage, ~taxonRank, ~scientificNameAuthorship, ~identificationQualifier, ~higherClassification, ~identificationReferences, ~typeStatus, ~previousIdentifications, ~identifiedBy, ~dateIdentified, ~decimalLatitude, ~decimalLongitude, ~verbatimLatitude, ~verbatimLongitude, ~stateProvince, ~country, ~continent, ~locality, ~island, ~county, ~municipality, ~countryCode, ~`dcterms:license`, ~eventDate, ~eventTime, ~day, ~month, ~year, ~basisOfRecord, ~`dcterms:type`, ~occurrenceStatus, ~recordNumber, ~recordedBy, ~eventID, ~samplingProtocol, ~samplingEffort, ~individualCount, ~organismQuantity, ~coordinatePrecision, ~coordinateUncertaintyInMeters, ~spatiallyValid, ~catalogNumber, ~datasetID, ~institutionCode, ~datasetName, ~otherCatalogNumbers, ~occurrenceID, ~collectionID, ~verbatimEventDate, ~associatedTaxa, ~associatedOrganisms, ~fieldNotes, ~sex, ~rights, ~rightsHolder, ~`dcterms:accessRights`, ~associatedReferences, ~`dcterms:bibliographicCitation`, ~references, ~informationWithheld, ~isDuplicateOf, ~assertions, ~occurrenceYear, ~duplicateStatus, ~associatedOccurrences, ~locationRemarks,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "australis", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -22.7, 133.4, NA, NA, "Northern Territory", "Australia", NA, "60 k S Ti Tree", NA, NA, NA, "AU", "CC-BY", "1996-10-02T14:00:00Z", NA, 3L, 10L, 1996L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157061", NA, "QM", NA, 2089363L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157061", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1995-12-31T13:00:00Z", NA, NA, NA,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "essingtoni", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -15.5, 128.7, NA, NA, "Western Australia", "Australia", NA, "Middle Springs 15k N Kunanurra", NA, NA, NA, "AU", "CC-BY", "1985-09-11T14:00:00Z", NA, 12L, 9L, 1985L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157059", NA, "QM", NA, 2089361L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157059", NA, NA, NA, NA, NA, "MALE", NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1984-12-31T13:00:00Z", NA, NA, NA,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "cassiae", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -23.7, 149.9, NA, NA, "Queensland", "Australia", NA, "Duaringa", NA, NA, NA, "AU", "CC-BY", "1987-09-06T14:00:00Z", NA, 7L, 9L, 1987L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157064", NA, "QM", NA, 2089366L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157064", NA, NA, NA, NA, NA, "MALE", NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1986-12-31T13:00:00Z", NA, NA, NA,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "australis", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -23.7, 149.9, NA, NA, "Queensland", "Australia", NA, "Duaringa", NA, NA, NA, "AU", "CC-BY", "1996-10-12T14:00:00Z", NA, 13L, 10L, 1996L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157060", NA, "QM", NA, 2089362L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157060", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1995-12-31T13:00:00Z", NA, NA, NA
)
write.csv(ALA_data, paste0(tempdir(), "/data.csv"), row.names = FALSE)
## GBIF data - this is data from not GBIF because GBIF data refused to be copy-pasted
GBIF_data <- dplyr::tribble(
~studyID, ~siteID, ~year, ~date, ~animalID, ~abundance, ~abundanceMethod, ~samplingMethod, ~numCensus, ~samplingIntensity, ~censusType, ~fieldDist, ~flowering, ~decimalLatitude, ~decimalLongitude, ~studyLocation, ~habitatType, ~siteDescription,
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon angelicus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon texanus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Anthophora californica", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina shinnersi", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina strenua", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Lasioglossum (Dialictus) sp.TX-14", 12L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden"
)
write.table(GBIF_data, paste0(tempdir(), "/occurrence.txt"), row.names = FALSE)
## iDigBio data - this is data from not iDigBio because iDigBio data refused to be copy-pasted
iDigBio_data <- dplyr::tribble(
~studyID, ~siteID, ~year, ~date, ~animalID, ~abundance, ~abundanceMethod, ~samplingMethod, ~numCensus, ~samplingIntensity, ~censusType, ~fieldDist, ~flowering, ~decimalLatitude, ~decimalLongitude, ~studyLocation, ~habitatType, ~siteDescription,
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon angelicus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon texanus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Anthophora californica", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina shinnersi", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina strenua", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Lasioglossum (Dialictus) sp.TX-14", 12L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden"
)
write.csv(iDigBio_data, paste0(tempdir(), "/occurrence_raw.csv"), row.names = FALSE)
## SCAN data
SCAN_data <- dplyr::tribble(
~id, ~institutionCode, ~collectionCode, ~ownerInstitutionCode, ~collectionID, ~basisOfRecord, ~occurrenceID, ~catalogNumber, ~otherCatalogNumbers, ~kingdom, ~phylum, ~class, ~order, ~family, ~scientificName, ~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,
13775122L, "CAS", "ANTWEB", "UCDC, Davis, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0106100", "casent0106100", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, NA, NA, NA, NA, NA, NA, NA, "P.S. Ward", NA, "6/28/05", 2005L, 6L, 28L, 179L, NA, "28 Jun 2005/29 Jun 2005", NA, NA, "PSW15443", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "pin", "United States", "California", NA, NA, "Davis", "coordinates obtained from Label", 38.54, -121.75667, NA, NA, NA, NA, NA, NA, NA, NA, 15L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 14:36", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:46a46727-6535-4e70-88e7-a42c98f806ed", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13775122",
13775123L, "CAS", "ANTWEB", "UCDC, Davis, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0106100-d01", "casent0106100-d01", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, NA, NA, NA, NA, NA, NA, NA, "P.S. Ward", NA, "6/28/05", 2005L, 6L, 28L, 179L, NA, "28 Jun 2005/29 Jun 2005", NA, NA, "PSW15443", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "100% EtOH", "United States", "California", NA, NA, "Davis", "coordinates obtained from Label", 38.54, -121.75667, NA, NA, NA, NA, NA, NA, NA, NA, 15L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 14:36", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:d6ff3ddb-4695-4aaf-ab89-c251ab2fc7e6", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13775123",
13775124L, "CAS", "ANTWEB", "UCDC, Davis, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0106100-d11", "casent0106100-d11", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, NA, NA, NA, NA, NA, NA, NA, "P.S. Ward", NA, "6/28/05", 2005L, 6L, 28L, 179L, NA, "28 Jun 2005/29 Jun 2005", NA, NA, "PSW15443", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "100% EtOH", "United States", "California", NA, NA, "Davis", "coordinates obtained from Label", 38.54, -121.75667, NA, NA, NA, NA, NA, NA, NA, NA, 15L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 14:36", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:4504a6e6-ab1c-4de7-ac43-a3588a63ae90", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13775124",
13852774L, "CAS", "ANTWEB", "CAS, San Francisco, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0249086", "casent0249086", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, "C. Schöning", NA, NA, NA, NA, NA, NA, "C. Schöning", NA, "9/1/09", 2009L, 9L, 1L, 244L, NA, "1-Sep-09", NA, NA, "N109-9", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "pin", "Kenya", NA, NA, NA, "Chogoria", NA, -0.20222, 37.50083, NA, NA, NA, NA, NA, NA, NA, NA, 2277L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 15:00", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:964139d3-fb07-4a57-9b7c-e9a5830f4c82", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13852774"
)
write.csv(SCAN_data, paste0(tempdir(), "/occurrences.csv"), row.names = FALSE)
# path to the test files goes here - load the thing, run the function
testOut <- BeeBDC::repoFinder(path = paste0(tempdir()))
# get variable type for each item in list
ALAout <- testOut[[1]]
GBIFout <- testOut[[2]]
iDigBioout <- testOut[[3]]
SCANout <- testOut[[4]]
# expected results - should all be present and all character values
testthat::test_that("repoFinder ALA expected", {
testthat::expect_type(ALAout, "character")
})
testthat::test_that("repoFinder GBIF expected", {
testthat::expect_type(GBIFout, "character")
})
testthat::test_that("repoFinder iDigBio expected", {
testthat::expect_type(iDigBioout, "character")
})
testthat::test_that("repoFinder SCAN expected", {
testthat::expect_type(SCANout, "character")
})
testthat::test_that("repoFinder expected class", {
testthat::expect_type(testOut, "list")
})
Try the BeeBDC package in your browser
Any scripts or data that you put into this service are public.
BeeBDC documentation built on Nov. 4, 2024, 9:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
requireNamespace("readr")
requireNamespace("BeeBDC")
# make some data files for repoFinder to search and save the files
## ALA data
ALA_data <- dplyr::tribble(
~scientificName, ~family, ~subfamily, ~genus, ~subgenus, ~subspecies, ~species, ~specificEpithet, ~infraspecificEpithet, ~acceptedNameUsage, ~taxonRank, ~scientificNameAuthorship, ~identificationQualifier, ~higherClassification, ~identificationReferences, ~typeStatus, ~previousIdentifications, ~identifiedBy, ~dateIdentified, ~decimalLatitude, ~decimalLongitude, ~verbatimLatitude, ~verbatimLongitude, ~stateProvince, ~country, ~continent, ~locality, ~island, ~county, ~municipality, ~countryCode, ~`dcterms:license`, ~eventDate, ~eventTime, ~day, ~month, ~year, ~basisOfRecord, ~`dcterms:type`, ~occurrenceStatus, ~recordNumber, ~recordedBy, ~eventID, ~samplingProtocol, ~samplingEffort, ~individualCount, ~organismQuantity, ~coordinatePrecision, ~coordinateUncertaintyInMeters, ~spatiallyValid, ~catalogNumber, ~datasetID, ~institutionCode, ~datasetName, ~otherCatalogNumbers, ~occurrenceID, ~collectionID, ~verbatimEventDate, ~associatedTaxa, ~associatedOrganisms, ~fieldNotes, ~sex, ~rights, ~rightsHolder, ~`dcterms:accessRights`, ~associatedReferences, ~`dcterms:bibliographicCitation`, ~references, ~informationWithheld, ~isDuplicateOf, ~assertions, ~occurrenceYear, ~duplicateStatus, ~associatedOccurrences, ~locationRemarks,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "australis", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -22.7, 133.4, NA, NA, "Northern Territory", "Australia", NA, "60 k S Ti Tree", NA, NA, NA, "AU", "CC-BY", "1996-10-02T14:00:00Z", NA, 3L, 10L, 1996L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157061", NA, "QM", NA, 2089363L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157061", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1995-12-31T13:00:00Z", NA, NA, NA,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "essingtoni", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -15.5, 128.7, NA, NA, "Western Australia", "Australia", NA, "Middle Springs 15k N Kunanurra", NA, NA, NA, "AU", "CC-BY", "1985-09-11T14:00:00Z", NA, 12L, 9L, 1985L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157059", NA, "QM", NA, 2089361L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157059", NA, NA, NA, NA, NA, "MALE", NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1984-12-31T13:00:00Z", NA, NA, NA,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "cassiae", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -23.7, 149.9, NA, NA, "Queensland", "Australia", NA, "Duaringa", NA, NA, NA, "AU", "CC-BY", "1987-09-06T14:00:00Z", NA, 7L, 9L, 1987L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157064", NA, "QM", NA, 2089366L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157064", NA, NA, NA, NA, NA, "MALE", NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1986-12-31T13:00:00Z", NA, NA, NA,
"APIDAE", "Apidae", NA, NA, NA, NA, NA, "australis", NA, NA, "family", NA, NA, NA, NA, NA, NA, NA, NA, -23.7, 149.9, NA, NA, "Queensland", "Australia", NA, "Duaringa", NA, NA, NA, "AU", "CC-BY", "1996-10-12T14:00:00Z", NA, 13L, 10L, 1996L, "PRESERVED_SPECIMEN", NA, "PRESENT", NA, NA, NA, NA, NA, NA, NA, NA, NA, TRUE, "T157060", NA, "QM", NA, 2089362L, "urn:lsid:ozcam.taxonomy.org.au:QM.Entomology:T157060", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "COORDINATE_UNCERTAINTY_METERS_INVALID | MISSING_GEOREFERENCEDBY | MISSING_GEOREFERENCEPROTOCOL | MISSING_GEOREFERENCESOURCES | MISSING_GEOREFERENCEVERIFICATIONSTATUS | MISSING_GEOREFERENCE_DATE | MISSING_TAXONRANK | TAXON_MATCH_HIGHERRANK", "1995-12-31T13:00:00Z", NA, NA, NA
)
write.csv(ALA_data, paste0(tempdir(), "/data.csv"), row.names = FALSE)
## GBIF data - this is data from not GBIF because GBIF data refused to be copy-pasted
GBIF_data <- dplyr::tribble(
~studyID, ~siteID, ~year, ~date, ~animalID, ~abundance, ~abundanceMethod, ~samplingMethod, ~numCensus, ~samplingIntensity, ~censusType, ~fieldDist, ~flowering, ~decimalLatitude, ~decimalLongitude, ~studyLocation, ~habitatType, ~siteDescription,
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon angelicus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon texanus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Anthophora californica", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina shinnersi", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina strenua", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Lasioglossum (Dialictus) sp.TX-14", 12L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden"
)
write.table(GBIF_data, paste0(tempdir(), "/occurrence.txt"), row.names = FALSE)
## iDigBio data - this is data from not iDigBio because iDigBio data refused to be copy-pasted
iDigBio_data <- dplyr::tribble(
~studyID, ~siteID, ~year, ~date, ~animalID, ~abundance, ~abundanceMethod, ~samplingMethod, ~numCensus, ~samplingIntensity, ~censusType, ~fieldDist, ~flowering, ~decimalLatitude, ~decimalLongitude, ~studyLocation, ~habitatType, ~siteDescription,
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon angelicus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Agapostemon texanus", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Anthophora californica", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina shinnersi", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Ceratina strenua", 1L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden",
"Ball01", "Bastrop Gardens", 2013L, "2013/5/22", "Lasioglossum (Dialictus) sp.TX-14", 12L, "Abundance", "Pan Trap", 1L, 24L, "50 pan traps (painted blue, yellow or left white as in LeBuhn et al) placed in x formation 1 m apart from center of the 50 m2 plot, vegetation measured as described for blue vane trapped.", "not measured", "flowering", 30.157397, -97.491703, "Bastrop, Bastrop County, TX", NA, "Agriculture. Community garden"
)
write.csv(iDigBio_data, paste0(tempdir(), "/occurrence_raw.csv"), row.names = FALSE)
## SCAN data
SCAN_data <- dplyr::tribble(
~id, ~institutionCode, ~collectionCode, ~ownerInstitutionCode, ~collectionID, ~basisOfRecord, ~occurrenceID, ~catalogNumber, ~otherCatalogNumbers, ~kingdom, ~phylum, ~class, ~order, ~family, ~scientificName, ~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,
13775122L, "CAS", "ANTWEB", "UCDC, Davis, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0106100", "casent0106100", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, NA, NA, NA, NA, NA, NA, NA, "P.S. Ward", NA, "6/28/05", 2005L, 6L, 28L, 179L, NA, "28 Jun 2005/29 Jun 2005", NA, NA, "PSW15443", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "pin", "United States", "California", NA, NA, "Davis", "coordinates obtained from Label", 38.54, -121.75667, NA, NA, NA, NA, NA, NA, NA, NA, 15L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 14:36", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:46a46727-6535-4e70-88e7-a42c98f806ed", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13775122",
13775123L, "CAS", "ANTWEB", "UCDC, Davis, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0106100-d01", "casent0106100-d01", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, NA, NA, NA, NA, NA, NA, NA, "P.S. Ward", NA, "6/28/05", 2005L, 6L, 28L, 179L, NA, "28 Jun 2005/29 Jun 2005", NA, NA, "PSW15443", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "100% EtOH", "United States", "California", NA, NA, "Davis", "coordinates obtained from Label", 38.54, -121.75667, NA, NA, NA, NA, NA, NA, NA, NA, 15L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 14:36", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:d6ff3ddb-4695-4aaf-ab89-c251ab2fc7e6", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13775123",
13775124L, "CAS", "ANTWEB", "UCDC, Davis, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0106100-d11", "casent0106100-d11", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, NA, NA, NA, NA, NA, NA, NA, "P.S. Ward", NA, "6/28/05", 2005L, 6L, 28L, 179L, NA, "28 Jun 2005/29 Jun 2005", NA, NA, "PSW15443", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "100% EtOH", "United States", "California", NA, NA, "Davis", "coordinates obtained from Label", 38.54, -121.75667, NA, NA, NA, NA, NA, NA, NA, NA, 15L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 14:36", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:4504a6e6-ab1c-4de7-ac43-a3588a63ae90", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13775124",
13852774L, "CAS", "ANTWEB", "CAS, San Francisco, CA, USA", "dc646193-9811-40ce-872a-f005f7dc059a", "PreservedSpecimen", "CAS:ANTWEB:casent0249086", "casent0249086", NA, "Animalia", "Arthropoda", "Insecta", "Hymenoptera", "apidae", "apis mellifera", 235783L, "Linnaeus, 1758", "Apis", "mellifera", NA, NA, "C. Schöning", NA, NA, NA, NA, NA, NA, "C. Schöning", NA, "9/1/09", 2009L, 9L, 1L, 244L, NA, "1-Sep-09", NA, NA, "N109-9", NA, NA, NA, NA, NA, NA, NA, NA, "worker", NA, NA, NA, "pin", "Kenya", NA, NA, NA, "Chogoria", NA, -0.20222, 37.50083, NA, NA, NA, NA, NA, NA, NA, NA, 2277L, NA, NA, NA, NA, NA, NA, NA, NA, "4/30/21 15:00", "http://creativecommons.org/publicdomain/zero/1.0/", "The California Academy of Sciences - AntWeb.org", NA, "urn:uuid:964139d3-fb07-4a57-9b7c-e9a5830f4c82", "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13852774"
)
write.csv(SCAN_data, paste0(tempdir(), "/occurrences.csv"), row.names = FALSE)
# path to the test files goes here - load the thing, run the function
testOut <- BeeBDC::repoFinder(path = paste0(tempdir()))
# get variable type for each item in list
ALAout <- testOut[[1]]
GBIFout <- testOut[[2]]
iDigBioout <- testOut[[3]]
SCANout <- testOut[[4]]
# expected results - should all be present and all character values
testthat::test_that("repoFinder ALA expected", {
testthat::expect_type(ALAout, "character")
})
testthat::test_that("repoFinder GBIF expected", {
testthat::expect_type(GBIFout, "character")
})
testthat::test_that("repoFinder iDigBio expected", {
testthat::expect_type(iDigBioout, "character")
})
testthat::test_that("repoFinder SCAN expected", {
testthat::expect_type(SCANout, "character")
})
testthat::test_that("repoFinder expected class", {
testthat::expect_type(testOut, "list")
})
Try the BeeBDC package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.