A cleaned dataset of occurrence records for azure jay (Cyanocorax caeruleus)
retrieved from the iDigBio using get_idigbio().
Records were cleaned using the package's internal duplicate-flagging workflow.
Format
A data frame containing georeferenced iDigBio occurrence records for C. caeruleus after all cleaning steps.
Examples
# First rows
head(occ_idig)
#> UberH3 aggs associatedsequences barcodevalue basisofrecord bed
#> 1 NA NA NULL NA machineobservation NA
#> 2 NA NA NULL NA preservedspecimen NA
#> 3 NA NA NULL NA preservedspecimen NA
#> 4 NA NA NULL NA preservedspecimen NA
#> 5 NA NA NULL NA machineobservation NA
#> 6 NA NA NULL NA preservedspecimen NA
#> canonicalname catalognumber class collectioncode
#> 1 cyanocorax caeruleus 0005478 aves fnjv
#> 2 cyanocorax caeruleus 29487 aves birds
#> 3 cyanocorax caeruleus 52342 aves birds
#> 4 cyanocorax caeruleus 12.crv.34 aves collection maës
#> 5 cyanocorax caeruleus 0050394 aves fnjv
#> 6 cyanocorax caeruleus 178589 aves orn
#> collectionid
#> 1 https://specieslink.net/col/238
#> 2 <NA>
#> 3 https://scientific-collections.gbif.org/collection/bf635c34-0569-4fb7-ad9c-91d821bac9e4
#> 4 1929.1
#> 5 https://specieslink.net/col/238
#> 6 <NA>
#> collectionname collector commonname commonnames
#> 1 NA alexandre luis padovan aleixo <NA> NULL
#> 2 NA <NA> <NA> NULL
#> 3 NA partridge, w h <NA> NULL
#> 4 NA sans collecteur <NA> NULL
#> 5 NA luiz dos anjos <NA> NULL
#> 6 NA camargo <NA> NULL
#> continent coordinateuncertainty country countrycode county
#> 1 south america NA brazil bra <NA>
#> 2 south america 1469 paraguay pry <NA>
#> 3 south america NA argentina arg <NA>
#> 4 <NA> NA <NA> <NA> <NA>
#> 5 south america NA brazil bra <NA>
#> 6 south america 3036 brazil bra <NA>
#> datasetid datecollected
#> 1 7ddf754f-d193-4cc9-b351-99906754a03b 1995-03-08T00:00:00+00:00
#> 2 7ddf754f-d193-4cc9-b351-99906754a03b 1901-08-23T00:00:00+00:00
#> 3 7ddf754f-d193-4cc9-b351-99906754a03b 1959-08-25T00:00:00+00:00
#> 4 <NA> 1909-06-25T00:00:00+00:00
#> 5 7ddf754f-d193-4cc9-b351-99906754a03b 2002-12-26T00:00:00+00:00
#> 6 7ddf754f-d193-4cc9-b351-99906754a03b 1934-10-10T00:00:00+00:00
#> datemodified dqs earliestageorloweststage
#> 1 2025-05-23T18:36:26.002398+00:00 0.2318841 NA
#> 2 2025-05-23T18:13:47.213183+00:00 0.2463768 NA
#> 3 2025-07-24T17:48:49.086870+00:00 0.3188406 NA
#> 4 2017-02-20T09:01:11.593455+00:00 0.2463768 NA
#> 5 2025-05-23T18:36:26.002398+00:00 0.2463768 NA
#> 6 2025-10-29T16:28:32.411713+00:00 0.2898551 NA
#> earliesteonorlowesteonothem earliestepochorlowestseries
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 NA <NA>
#> 4 NA <NA>
#> 5 NA <NA>
#> 6 NA <NA>
#> earliesteraorlowesterathem earliestperiodorlowestsystem
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 NA <NA>
#> 4 NA <NA>
#> 5 NA <NA>
#> 6 NA <NA>
#> etag eventdate family fieldnumber
#> 1 d4cd02bb4a594a94541a6af6dcad819a10015103 1995-03-08 corvidae <NA>
#> 2 b6bf9b574b4c9b53e4de4f85a713b1c9cbb8f1c6 1901-08-23 corvidae <NA>
#> 3 c886e564e36d73ce63fc051b52c121662d7b8c96 1959-08-25 corvidae <NA>
#> 4 cfac449459e9f92f607d77141bea36968ed2da8d 1909-6-25 corvidae <NA>
#> 5 8a84b83ceee954cc5f0a5a792f5904abf49312db 2002-12-26 corvidae <NA>
#> 6 cd336080ae997a693fc65558fca43abd9f1311f6 1934-10-10 corvidae <NA>
#> flags
#> 1 dwc_taxonrank_added, dwc_multimedia_added, gbif_reference_added, idigbio_isocountrycode_added, gbif_canonicalname_added, dwc_taxonomicstatus_added, gbif_genericname_added, dwc_datasetid_added, dwc_continent_added, dwc_parentnameusageid_added, dwc_scientificnameauthorship_added, dwc_taxonid_added, gbif_vernacularname_added, gbif_taxon_corrected, dwc_order_added
#> 2 dwc_scientificnameauthorship_added, dwc_taxonrank_replaced, dwc_taxonomicstatus_added, gbif_genericname_added, dwc_datasetid_added, gbif_taxon_corrected, dwc_multimedia_added, dwc_taxonid_added, idigbio_isocountrycode_added, gbif_vernacularname_added, gbif_canonicalname_added, gbif_reference_added, dwc_parentnameusageid_added
#> 3 geopoint_low_precision, dwc_multimedia_added, dwc_taxonrank_replaced, dwc_taxonomicstatus_added, gbif_genericname_added, dwc_datasetid_added, gbif_taxon_corrected, dwc_parentnameusageid_added, dwc_scientificnameauthorship_added, dwc_taxonid_added, idigbio_isocountrycode_added, gbif_vernacularname_added, gbif_canonicalname_added, gbif_reference_added
#> 4 geopoint_datum_missing
#> 5 dwc_taxonrank_added, dwc_multimedia_added, gbif_reference_added, dwc_scientificnameauthorship_added, idigbio_isocountrycode_added, gbif_canonicalname_added, dwc_taxonomicstatus_added, gbif_genericname_added, dwc_datasetid_added, dwc_continent_added, dwc_parentnameusageid_added, dwc_taxonid_added, gbif_vernacularname_added, gbif_taxon_corrected, dwc_order_added
#> 6 geopoint_datum_error, rev_geocode_eez, dwc_taxonrank_added, gbif_reference_added, gbif_genericname_added, dwc_datasetid_added, dwc_scientificnameauthorship_replaced, gbif_vernacularname_added, dwc_parentnameusageid_added, idigbio_isocountrycode_added, dwc_taxonomicstatus_added, dwc_taxonid_added, dwc_multimedia_added, gbif_taxon_corrected, gbif_canonicalname_added
#> formation genus geologicalcontextid lon lat group hasImage
#> 1 NA cyanocorax NA NA NA NA FALSE
#> 2 NA cyanocorax NA -56.95254 -25.66729 NA FALSE
#> 3 NA cyanocorax NA -53.90000 -26.47000 NA FALSE
#> 4 NA cyanocorax NA -46.63639 -23.54770 NA FALSE
#> 5 NA cyanocorax NA -51.33667 -23.76056 NA FALSE
#> 6 NA cyanocorax NA -47.95000 -25.01667 NA FALSE
#> hasMedia
#> 1 FALSE
#> 2 FALSE
#> 3 FALSE
#> 4 FALSE
#> 5 FALSE
#> 6 FALSE
#> highertaxon
#> 1 <NA>
#> 2 <NA>
#> 3 animalia | chordata | aves | passeriformes | corvidae | cyanocorax
#> 4 <NA>
#> 5 <NA>
#> 6 animalia chordata vertebrata aves neornithes passeriformes oscines corvidae cyanocorax caeruleus
#> highestbiostratigraphiczone individualcount infraspecificepithet
#> 1 NA 1 NA
#> 2 NA NA NA
#> 3 NA NA NA
#> 4 NA 1 NA
#> 5 NA NA NA
#> 6 NA 1 NA
#> institutioncode
#> 1 unicamp
#> 2 ummz
#> 3 lacm
#> 4 boum
#> 5 unicamp
#> 6 mcz
#> institutionid
#> 1 <NA>
#> 2 <NA>
#> 3 https://scientific-collections.gbif.org/institution/2fc908ba-e775-49e2-bffe-6b9041c3b70f
#> 4 <NA>
#> 5 <NA>
#> 6 b4640710-8e03-11d8-b956-b8a03c50a862
#> institutionname kingdom latestageorhigheststage latesteonorhighesteonothem
#> 1 NA animalia NA NA
#> 2 NA animalia NA NA
#> 3 NA animalia NA NA
#> 4 NA animalia NA NA
#> 5 NA animalia NA NA
#> 6 NA animalia NA NA
#> latestepochorhighestseries latesteraorhighesterathem
#> 1 NA NA
#> 2 NA NA
#> 3 NA NA
#> 4 NA NA
#> 5 NA NA
#> 6 NA NA
#> latestperiodorhighestsystem lithostratigraphicterms
#> 1 NA NA
#> 2 NA NA
#> 3 NA NA
#> 4 NA NA
#> 5 NA NA
#> 6 NA NA
#> locality
#> 1 parque estadual intervales
#> 2 sapucay
#> 3 tobunas
#> 4 sao paulo
#> 5 fragmento florestal próximo ao parque estadual mata dos godoy
#> 6 cananea
#> lowestbiostratigraphiczone maxdepth maxelevation mediarecords member mindepth
#> 1 NA NA NA NULL NA NA
#> 2 NA NA NA NULL NA NA
#> 3 NA NA NA NULL NA NA
#> 4 NA NA 760 NULL NA NA
#> 5 NA NA NA NULL NA NA
#> 6 NA NA NA NULL NA NA
#> minelevation municipality occurrenceid
#> 1 NA sete barras https://specieslink.net/guid/238/0005478
#> 2 NA <NA> b3101421-f924-11e2-b158-782bcb84bc75
#> 3 NA <NA> 5bf19932-d3e8-46db-b996-53379ca09ca5
#> 4 NA <NA> 12.crv.34
#> 5 NA londrina https://specieslink.net/guid/238/0050394
#> 6 NA <NA> mcz:orn:178589
#> order phylum query
#> 1 passeriformes chordata NA
#> 2 passeriformes chordata NA
#> 3 passeriformes chordata NA
#> 4 passeriformes chordata NA
#> 5 passeriformes chordata NA
#> 6 passeriformes chordata NA
#> recordids
#> 1 5caa5b0d-24b7-4c69-9c7b-089f343b7efc\\https://specieslink.net/guid/238/0005478
#> 2 4a32531f-1580-499f-bd48-5b0ef4cc5722\\urn:catalog:ummz:birds:29487, 4a32531f-1580-499f-bd48-5b0ef4cc5722\\b3101421-f924-11e2-b158-782bcb84bc75
#> 3 2d853a6d-50ec-4931-8e91-48fc2491fdee\\5bf19932-d3e8-46db-b996-53379ca09ca5
#> 4 3172ee72-4b10-4d6b-b4b3-f3319b25c60d\\12.crv.34
#> 5 5caa5b0d-24b7-4c69-9c7b-089f343b7efc\\https://specieslink.net/guid/238/0050394
#> 6 271a9ce9-c6d3-4b63-a722-cb0adc48863f\\mcz:orn:178589
#> recordnumber recordset scientificname size
#> 1 <NA> 5caa5b0d-24b7-4c69-9c7b-089f343b7efc Cyanocorax caeruleus NA
#> 2 <NA> 4a32531f-1580-499f-bd48-5b0ef4cc5722 Cyanocorax caeruleus NA
#> 3 19784 2d853a6d-50ec-4931-8e91-48fc2491fdee Cyanocorax caeruleus NA
#> 4 <NA> 3172ee72-4b10-4d6b-b4b3-f3319b25c60d Cyanocorax caeruleus NA
#> 5 <NA> 5caa5b0d-24b7-4c69-9c7b-089f343b7efc Cyanocorax caeruleus NA
#> 6 <NA> 271a9ce9-c6d3-4b63-a722-cb0adc48863f Cyanocorax caeruleus NA
#> specificepithet startdayofyear stateprovince taxonid taxonomicstatus
#> 1 caeruleus 67 são paulo 2482560 accepted
#> 2 caeruleus 235 paraguari 2482560 accepted
#> 3 caeruleus 237 misiones prov 2482560 accepted
#> 4 caeruleus 176 <NA> 2482560 accepted
#> 5 caeruleus 360 paraná 2482560 accepted
#> 6 caeruleus 283 sao paulo 2482560 accepted
#> taxonrank typestatus uuid verbatimeventdate
#> 1 species <NA> 000d87f1-db3e-4784-91d2-91aec34abf85 <NA>
#> 2 species <NA> 02ffadca-502b-469f-8d4a-299a7d8e91a5 <NA>
#> 3 species <NA> 0408655e-5896-4e2e-8507-becfd903a0e1 25 aug 1959
#> 4 species <NA> 0538e125-8fa4-412b-89c8-a44f38f46731 1909, 25 juin
#> 5 species <NA> 0ccf5483-4c82-4214-aa7b-3e2523fddde6 <NA>
#> 6 species <NA> 0d86f91a-6916-4432-93b1-d18c36cf015d 10/10/1934
#> verbatimlocality version waterbody
#> 1 <NA> NA <NA>
#> 2 <NA> NA <NA>
#> 3 | south america | argentina | misiones prov | | tobunas NA <NA>
#> 4 <NA> NA <NA>
#> 5 <NA> NA <NA>
#> 6 south america, brazil, sao paulo, cananea NA <NA>
# Number of cleaned records
nrow(occ_idig)
#> [1] 33