spocc = SPecies OCCurrence data
At rOpenSci, we have been writing R packages to interact with many sources of species occurrence data, including GBIF, Vertnet, BISON, iNaturalist, the Berkeley ecoengine, AntWeb. spocc is an R package to query and collect species occurrence data from many sources. The goal is to wrap functions in other R packages to make a seamless experience across data sources for the user.
The inspiration for this comes from users requesting a more seamless experience across data sources, and from our work on a similar package for taxonomy data (taxize).
BEWARE: In cases where you request data from multiple providers, especially when including GBIF, there could be duplicate records since many providers' data eventually ends up with GBIF. See ?spocc_duplicates, after installation, for more.
See CONTRIBUTING.md
Stable version from CRAN
install.packages("spocc", dependencies = TRUE)Or the development version from GitHub
install.packages("devtools")
devtools::install_github("ropensci/spocc")library("spocc")Get data from GBIF
(out <- occ(query='Accipiter striatus', from='gbif', limit=100))
#> Searched: gbif
#> Occurrences - Found: 447,930, Returned: 100
#> Search type: Scientific
#> gbif: Accipiter striatus (100)out$gbif # just gbif data
#> Species [Accipiter striatus (100)]
#> First 10 rows of [Accipiter_striatus]
#>
#> name longitude latitude prov
#> 1 Accipiter striatus -97.64102 30.55880 gbif
#> 2 Accipiter striatus -104.83266 21.47117 gbif
#> 3 Accipiter striatus -75.17209 40.34000 gbif
#> 4 Accipiter striatus -78.11608 37.98438 gbif
#> 5 Accipiter striatus 0.00000 0.00000 gbif
#> 6 Accipiter striatus -97.25801 32.89462 gbif
#> 7 Accipiter striatus -72.54554 41.22175 gbif
#> 8 Accipiter striatus -71.06930 42.34816 gbif
#> 9 Accipiter striatus -99.47478 27.48211 gbif
#> 10 Accipiter striatus -109.95193 23.79093 gbif
#> .. ... ... ... ...
#> Variables not shown: issues (chr), key (int), datasetKey (chr),
#> publishingOrgKey (chr), publishingCountry (chr), protocol (chr),
#> lastCrawled (chr), lastParsed (chr), extensions (chr), basisOfRecord
#> (chr), taxonKey (int), kingdomKey (int), phylumKey (int), classKey
#> (int), orderKey (int), familyKey (int), genusKey (int), speciesKey
#> (int), scientificName (chr), kingdom (chr), phylum (chr), order
#> (chr), family (chr), genus (chr), species (chr), genericName (chr),
#> specificEpithet (chr), taxonRank (chr), dateIdentified (chr), year
#> (int), month (int), day (int), eventDate (time), modified (chr),
#> lastInterpreted (chr), references (chr), identifiers (chr), facts
#> (chr), relations (chr), geodeticDatum (chr), class (chr), countryCode
#> (chr), country (chr), rightsHolder (chr), identifier (chr),
#> informationWithheld (chr), verbatimEventDate (chr), datasetName
#> (chr), collectionCode (chr), verbatimLocality (chr), gbifID (chr),
#> occurrenceID (chr), taxonID (chr), recordedBy (chr), catalogNumber
#> (chr), http...unknown.org.occurrenceDetails (chr), institutionCode
#> (chr), rights (chr), eventTime (chr), identificationID (chr),
#> occurrenceRemarks (chr), sex (chr), establishmentMeans (chr),
#> continent (chr), stateProvince (chr), institutionID (chr), county
#> (chr), language (chr), type (chr), preparations (chr),
#> occurrenceStatus (chr), higherGeography (chr), nomenclaturalCode
#> (chr), endDayOfYear (chr), locality (chr), disposition (chr),
#> otherCatalogNumbers (chr), startDayOfYear (chr), accessRights (chr),
#> higherClassification (chr), dynamicProperties (chr),
#> identificationVerificationStatus (chr), locationAccordingTo (chr),
#> identifiedBy (chr), georeferencedDate (chr), georeferencedBy (chr),
#> georeferenceProtocol (chr), georeferenceVerificationStatus (chr),
#> verbatimCoordinateSystem (chr), individualID (chr),
#> previousIdentifications (chr), identificationQualifier (chr),
#> samplingProtocol (chr), georeferenceSources (chr), elevation (dbl),
#> elevationAccuracy (dbl), lifeStage (chr), scientificNameID (chr),
#> georeferenceRemarks (chr), source (chr), fieldNotes (chr), waterBody
#> (chr), recordNumber (chr), samplingEffort (chr), locationRemarks
#> (chr), infraspecificEpithet (chr), collectionID (chr),
#> ownerInstitutionCode (chr), datasetID (chr), verbatimElevation (chr),
#> vernacularName (chr)Get fine-grained detail over each data source by passing on parameters to the packge rebird in this example.
out <- occ(query='Setophaga caerulescens', from='ebird', ebirdopts=list(region='US'))
out$ebird # just ebird data
#> Species [Setophaga caerulescens (500)]
#> First 10 rows of [Setophaga_caerulescens]
#>
#> name longitude latitude prov
#> 1 Setophaga caerulescens -88.14688 39.46639 ebird
#> 2 Setophaga caerulescens -71.16393 42.65060 ebird
#> 3 Setophaga caerulescens -83.21080 39.90013 ebird
#> 4 Setophaga caerulescens -80.30560 25.62582 ebird
#> 5 Setophaga caerulescens -79.91361 32.74346 ebird
#> 6 Setophaga caerulescens -76.43384 43.31383 ebird
#> 7 Setophaga caerulescens -78.80536 36.06608 ebird
#> 8 Setophaga caerulescens -75.18879 39.86365 ebird
#> 9 Setophaga caerulescens -80.34590 36.81220 ebird
#> 10 Setophaga caerulescens -77.04935 38.95550 ebird
#> .. ... ... ... ...
#> Variables not shown: comName (chr), howMany (int), locID (chr), locName
#> (chr), locationPrivate (lgl), obsDt (time), obsReviewed (lgl),
#> obsValid (lgl)Get data from many sources in a single call
ebirdopts = list(region='US'); gbifopts = list(country='US')
out <- occ(query='Setophaga caerulescens', from=c('gbif','bison','inat','ebird'), gbifopts=gbifopts, ebirdopts=ebirdopts, limit=50)
head(occ2df(out)); tail(occ2df(out))
#> name longitude latitude prov date
#> 1 Setophaga caerulescens -80.82181 24.81413 gbif 2015-03-26 23:00:00
#> 2 Setophaga caerulescens -82.55674 35.63396 gbif 2015-04-21 18:51:02
#> 3 Setophaga caerulescens -81.69378 36.14885 gbif 2015-05-01 22:00:00
#> 4 Setophaga caerulescens -83.19085 41.62769 gbif 2015-05-16 22:00:00
#> 5 Setophaga caerulescens -82.87321 24.62802 gbif 2015-05-06 22:00:00
#> 6 Setophaga caerulescens -77.07069 38.83192 gbif 2015-05-08 12:09:00
#> key
#> 1 1088930021
#> 2 1088954620
#> 3 1122965432
#> 4 1092893939
#> 5 1092893709
#> 6 1088980026
#> name longitude latitude prov date
#> 195 Setophaga caerulescens -78.01059 40.53442 ebird 2015-09-11 06:58:00
#> 196 Setophaga caerulescens -75.39042 40.63633 ebird 2015-09-11 06:55:00
#> 197 Setophaga caerulescens -76.47900 42.46045 ebird 2015-09-11 06:54:00
#> 198 Setophaga caerulescens -77.04298 38.95766 ebird 2015-09-11 06:50:00
#> 199 Setophaga caerulescens -77.05141 38.95940 ebird 2015-09-11 06:45:00
#> 200 Setophaga caerulescens -77.04676 38.96532 ebird 2015-09-11 06:45:00
#> key
#> 195 L2354489
#> 196 L372101
#> 197 L287796
#> 198 L283552
#> 199 L280792
#> 200 L599606All mapping functionality is now in a separate package spoccutils, to make spocc easier to maintain.
- Please report any issues or bugs.
- License: MIT
- Get citation information for
spoccin R doingcitation(package = 'spocc') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
