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: 447,905, 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 0.00000 0.00000 gbif
#> 2 Accipiter striatus NA NA gbif
#> 3 Accipiter striatus -104.88120 21.46585 gbif
#> 4 Accipiter striatus -71.19554 42.31845 gbif
#> 5 Accipiter striatus -78.15051 37.95521 gbif
#> 6 Accipiter striatus -97.80459 30.41678 gbif
#> 7 Accipiter striatus -75.17209 40.34000 gbif
#> 8 Accipiter striatus -122.20175 37.88370 gbif
#> 9 Accipiter striatus -99.47894 27.44924 gbif
#> 10 Accipiter striatus -135.32701 57.05420 gbif
#> .. ... ... ... ...
#> Variables not shown: issues (chr), key (int), datasetKey (chr),
#> publishingOrgKey (chr), publishingCountry (chr), protocol (chr),
#> lastCrawled (chr), lastParsed (chr), extensions (chr), basisOfRecord
#> (chr), sex (chr), establishmentMeans (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), continent (chr), stateProvince (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), startDayOfYear (chr), verbatimEventDate (chr),
#> preparations (chr), institutionID (chr), verbatimLocality (chr),
#> nomenclaturalCode (chr), higherClassification (chr), rights (chr),
#> higherGeography (chr), occurrenceID (chr), type (chr), collectionCode
#> (chr), occurrenceRemarks (chr), gbifID (chr), accessRights (chr),
#> institutionCode (chr), endDayOfYear (chr), county (chr),
#> catalogNumber (chr), otherCatalogNumbers (chr), occurrenceStatus
#> (chr), locality (chr), language (chr), identifier (chr), disposition
#> (chr), dateIdentified (chr), informationWithheld (chr),
#> http...unknown.org.occurrenceDetails (chr), rightsHolder (chr),
#> taxonID (chr), datasetName (chr), recordedBy (chr), identificationID
#> (chr), eventTime (chr), georeferencedDate (chr), georeferenceSources
#> (chr), identifiedBy (chr), identificationVerificationStatus (chr),
#> samplingProtocol (chr), georeferenceVerificationStatus (chr),
#> individualID (chr), locationAccordingTo (chr),
#> verbatimCoordinateSystem (chr), previousIdentifications (chr),
#> georeferenceProtocol (chr), identificationQualifier (chr),
#> dynamicProperties (chr), georeferencedBy (chr), lifeStage (chr),
#> elevation (dbl), elevationAccuracy (dbl), 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 -72.00877 43.44167 ebird
#> 2 Setophaga caerulescens -71.71499 44.82760 ebird
#> 3 Setophaga caerulescens -69.24381 46.10138 ebird
#> 4 Setophaga caerulescens -83.48799 35.02802 ebird
#> 5 Setophaga caerulescens -71.73941 44.76401 ebird
#> 6 Setophaga caerulescens -86.01660 44.75613 ebird
#> 7 Setophaga caerulescens -73.99459 44.30380 ebird
#> 8 Setophaga caerulescens -80.27513 38.19799 ebird
#> 9 Setophaga caerulescens -74.03718 42.20338 ebird
#> 10 Setophaga caerulescens -73.88611 44.51111 ebird
#> .. ... ... ... ...
#> Variables not shown: comName (chr), howMany (dbl), 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))
#> Error in mapply(FUN = f, ..., SIMPLIFY = FALSE): object 'id' not found
#> Error in mapply(FUN = f, ..., SIMPLIFY = FALSE): object 'id' not foundAll mapping functionality is now in a separate package spoccutils, to make spocc easier to maintain.
spocc in R doing citation(package = 'spocc')