The function bison() is sort of the main interface to searching for data in rbison, covered in the vignette rbison introduction. However, there are many other functions.
library('rbison')
BISON exposes an API supporting access to Data Provider and Resource based data access statistics.
out <- bison_stats(what='wms')
out$Arctos
#> $name
#> [1] "Arctos"
#>
#> $resources
#> [1] "Bird tissues, Division of Genomic Resources, UNM, Albuquerque, NM."
#> [2] "Fish tissues, Division of Genomic Resources, UNM, Albuquerque, NM."
#> [3] "Harold W. Manter Laboratory of Parasitology Collection"
#> [4] "KNWR Entomology Collection"
#> [5] "KNWR Herbarium Collection"
#> [6] "Kenelm W. Philip lepidoptera collection"
#> [7] "Mammal tissues, Division of Genomic Resources, UNM, Albuquerque, NM."
#> [8] "STAMP seabird egg collection"
#> [9] "U. S. National Parasite Collection's holdings from Robert L. Rausch"
#>
#> $data
#> providerId resourceId lastUpdated todayTotals currentWeekTotals
#> 1 177 177,973 NA 0 0
#> 2 177 177,988 NA 0 0
#> 3 177 177,13472 NA 342 803
#> 4 177 177,13468 NA 48 713
#> 5 177 177,13474 NA 0 266
#> 6 177 177,976 NA 0 266
#> 7 177 177,972 NA 0 0
#> 8 177 177,971 NA 0 266
#> 9 177 177,14394 NA 0 266
#> yesterdayTotals lastWeekTotals janTotals febTotals marTotals aprTotals
#> 1 0 0 0 0 0 0
#> 2 0 0 0 0 0 0
#> 3 342 1107 14021 15635 10641 1910
#> 4 48 867 11480 11197 10135 1580
#> 5 0 809 8960 7536 6106 1075
#> 6 0 831 8865 7346 5097 1097
#> 7 0 0 0 0 0 0
#> 8 0 831 9032 7620 5198 1097
#> 9 0 831 8382 7148 5091 1097
#> mayTotals junTotals julTotals augTotals sepTotals octTotals novTotals
#> 1 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0
#> 3 0 0 0 0 0 0 0
#> 4 0 0 0 0 0 0 0
#> 5 0 0 0 0 0 0 0
#> 6 0 0 0 0 0 0 0
#> 7 0 0 0 0 0 0 0
#> 8 0 0 0 0 0 0 0
#> 9 0 0 0 0 0 0 0
#> decTotals currentMonthTotals id type
#> 1 0 0 NA wms
#> 2 0 0 NA wms
#> 3 0 1910 NA wms
#> 4 0 1580 NA wms
#> 5 0 1075 NA wms
#> 6 0 1097 NA wms
#> 7 0 0 NA wms
#> 8 0 1097 NA wms
#> 9 0 1097 NA wms
out$Harvard_University_Herbaria
#> $name
#> [1] "Harvard University Herbaria"
#>
#> $resources
#> [1] "E.C. Smith Herbarium" "Harvard University Herbaria"
#>
#> $data
#> providerId resourceId lastUpdated todayTotals currentWeekTotals
#> 1 214 214,1829 NA 0 0
#> 2 214 214,202435 NA 1196 1639
#> yesterdayTotals lastWeekTotals janTotals febTotals marTotals aprTotals
#> 1 0 0 0 0 0 0
#> 2 1196 966 17673 17172 12708 2605
#> mayTotals junTotals julTotals augTotals sepTotals octTotals novTotals
#> 1 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0
#> decTotals currentMonthTotals id type
#> 1 0 0 NA wms
#> 2 0 2605 NA wms
out$ZooKeys
#> $name
#> [1] "ZooKeys"
#>
#> $resources
#> [1] "Localities for the arachnid genus Acuclavella (Opiliones, Ceratolasmatidae)"
#> [2] "Megophthalmidia_of_North_America"
#> [3] "USBombus, contemporary survey data of North American bumble bees (Hymenoptera, Apidae, Bombus) distributed in the United States"
#> [4] "Western Palaearctic Ectoedemia (Zimmermannia) Hering and Ectoedemia Busck s. str. (Lepidoptera: Nepticulidae): five new species and new data on distribution, hostplants and recognition"
#>
#> $data
#> providerId resourceId lastUpdated todayTotals currentWeekTotals
#> 1 300 300,15002 NA 0 266
#> 2 300 300,201848 NA 126 392
#> 3 300 300,202310 NA 198 778
#> 4 300 300,13716 NA 0 0
#> yesterdayTotals lastWeekTotals janTotals febTotals marTotals aprTotals
#> 1 0 870 8262 7455 5322 1136
#> 2 126 831 8066 9182 5343 1223
#> 3 198 1071 12766 15254 11328 1849
#> 4 0 17 140 3 56 17
#> mayTotals junTotals julTotals augTotals sepTotals octTotals novTotals
#> 1 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0
#> 3 0 0 0 0 0 0 0
#> 4 0 0 0 0 0 0 0
#> decTotals currentMonthTotals id type
#> 1 0 1136 NA wms
#> 2 0 1223 NA wms
#> 3 0 1849 NA wms
#> 4 0 17 NA wms
head(bison_providers(provider_no=131))
#> id
#> 1 131
#> 2 131,11420
#> 3 131,595
#> 4 131,202619
#> 5 131,14537
#> 6 131,14526
#> name
#> 1 http //www.kahaku.go.jp/english/ National Museum of Nature and Science, Japan
#> 2 Akita Prefectural Museum Hiroki Watanabe Collection of mollusca
#> 3 Algae Collection of National Museum of Nature and Science
#> 4 Annelida collection of National Museum of Nature and Science
#> 5 Arthropoda Collection of the Seto Marine Biological Laboratory, Kyoto University
#> 6 Bacteria Collection of the Seto Marine Biological Laboratory, Kyoto University
out <- bison_providers(details=TRUE)
out$National_Herbarium_of_New_South_Wales
#> provider_name
#> 1 National Herbarium of New South Wales
#> 2 National Herbarium of New South Wales
#> provider_url name
#> 1 https://bison.usgs.gov/api/providers/details NSW herbarium collection
#> 2 https://bison.usgs.gov/api/providers/details Plants of Papua New Guinea
#> id url
#> 1 126,968 http://plantnet.rbgsyd.nsw.gov.au
#> 2 126,969 http://plantnet.rbgsyd.nsw.gov.au/PNGplants
Search for and collect taxonomic name data from the USGS Bison API using solr.
bison_tax(query="*bear")
#> $numFound
#> [1] 48
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 Louisiana black bear Louisiana black bear
#> 2 Sloth Bear Sloth Bear
#> 3 grizzly bear grizzly bear
#> 4 bear oak bear oak
#> 5 yellow woollybear yellow woollybear
#> 6 bear daisy bear daisy
#> 7 banded woollybear banded woollybear
#> 8 Asiatic black bear Asiatic black bear
#> 9 Kodiak bear Kodiak bear
#> 10 black-ended bear black-ended bear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
Exact argument, here nothing found with latter call as '*bear' doesn't exist, which makes sense
bison_tax(query="*bear", exact=FALSE)
#> $numFound
#> [1] 48
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 Louisiana black bear Louisiana black bear
#> 2 Sloth Bear Sloth Bear
#> 3 grizzly bear grizzly bear
#> 4 bear oak bear oak
#> 5 yellow woollybear yellow woollybear
#> 6 bear daisy bear daisy
#> 7 banded woollybear banded woollybear
#> 8 Asiatic black bear Asiatic black bear
#> 9 Kodiak bear Kodiak bear
#> 10 black-ended bear black-ended bear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
bison_tax(query="*bear", exact=TRUE)
#> $numFound
#> [1] 46
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 Sloth Bear Sloth Bear
#> 2 grizzly bear grizzly bear
#> 3 bear oak bear oak
#> 4 bear daisy bear daisy
#> 5 Kodiak bear Kodiak bear
#> 6 Grizzly Bear Grizzly Bear
#> 7 black bear black bear
#> 8 bear garlic bear garlic
#> 9 bear sedge bear sedge
#> 10 bear huckleberry bear huckleberry
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
Using solr arguments (not all Solr arguments work). Return a certain number of rows
bison_tax(query="*bear", method="vernacularName", rows=3)
#> $numFound
#> [1] 48
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 Louisiana black bear Louisiana black bear
#> 2 Sloth Bear Sloth Bear
#> 3 grizzly bear grizzly bear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
Return certain fields
bison_tax(query="*bear", method="vernacularName", fl='vernacularName')
#> $numFound
#> [1] 48
#>
#> $names
#> vernacularName
#> 1 Louisiana black bear
#> 2 Sloth Bear
#> 3 grizzly bear
#> 4 bear oak
#> 5 yellow woollybear
#> 6 bear daisy
#> 7 banded woollybear
#> 8 Asiatic black bear
#> 9 Kodiak bear
#> 10 black-ended bear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
Search for and collect occurrence data from the USGS Bison API using their solr endpoint.
bison_solr(scientificName='Ursus americanus', computedStateFips='02',
fl="scientificName", rows=3)
#> $num_found
#> [1] 1055
#>
#> $points
#> scientificName
#> 1 Ursus americanus
#> 2 Ursus americanus
#> 3 Ursus americanus
#>
#> $highlight
#> NULL
#>
#> $facets
#> $facets$facet_queries
#> NULL
#>
#> $facets$facet_fields
#> NULL
#>
#> $facets$facet_dates
#> NULL
#>
#> $facets$facet_ranges
#> NULL
#>
#>
#> attr(,"class")
#> [1] "bison_solr"
bison_solr(scientificName='Ursus americanus', computedStateFips='02',
rows=3, fl="scientificName,decimalLongitude,decimalLatitude")
#> $num_found
#> [1] 1055
#>
#> $points
#> decimalLongitude scientificName decimalLatitude
#> 1 -150.55 Ursus americanus 59.59
#> 2 -150.55 Ursus americanus 59.59
#> 3 -149.66 Ursus americanus 59.83
#>
#> $highlight
#> NULL
#>
#> $facets
#> $facets$facet_queries
#> NULL
#>
#> $facets$facet_fields
#> NULL
#>
#> $facets$facet_dates
#> NULL
#>
#> $facets$facet_ranges
#> NULL
#>
#>
#> attr(,"class")
#> [1] "bison_solr"
bison_solr(TSNs = 174670, rows=2)$points[,1:6]
#> eventDate providedScientificName countryCode providedCounty ambiguous
#> 1 Pelecaniformes US Polk FALSE
#> 2 Pelecaniformes US Polk FALSE
#> verbatimLocality
#> 1
#> 2
bison_solr(kingdom = "Plantae", rows=2)$points[,1:6]
#> eventDate providedScientificName year
#> 1 1987-06-17T02:00Z Elymus glaucus subsp. virescens (Piper) Gould 1987
#> 2 Elymus hansenii Scribn. NA
#> countryCode providedCounty ambiguous
#> 1 US San Diego TRUE
#> 2 US San Diego TRUE
Using additional solr fields - Faceting
bison_solr(scientificName='Helianthus annuus', rows=0, facet='true',
facet.field='computedStateFips')
#> $num_found
#> [1] 5982
#>
#> $points
#> NULL
#>
#> $highlight
#> NULL
#>
#> $facets
#> $facets$facet_queries
#> NULL
#>
#> $facets$facet_fields
#> $facets$facet_fields$computedStateFips
#> X1 X2
#> 1 06 773
#> 2 48 500
#> 3 20 350
#> 4 08 299
#> 5 46 188
#> 6 35 150
#> 7 31 120
#> 8 49 112
#> 9 30 102
#> 10 38 102
#> 11 04 93
#> 12 16 86
#> 13 17 86
#> 14 29 86
#> 15 40 77
#> 16 56 77
#> 17 41 68
#> 18 53 45
#> 19 19 43
#> 20 32 41
#> 21 26 35
#> 22 05 34
#> 23 39 33
#> 24 09 31
#> 25 22 31
#> 26 27 25
#> 27 25 24
#> 28 47 24
#> 29 AB 24
#> 30 BC 22
#> 31 12 21
#> 32 21 21
#> 33 SK 21
#> 34 18 20
#> 35 42 19
#> 36 36 16
#> 37 37 16
#> 38 45 13
#> 39 34 11
#> 40 23 10
#> 41 54 10
#> 42 50 8
#> 43 55 8
#> 44 24 7
#> 45 13 6
#> 46 ON 6
#> 47 01 5
#> 48 28 5
#> 49 33 5
#> 50 MB 5
#> 51 02 4
#> 52 11 4
#> 53 QC 4
#> 54 10 3
#> 55 44 3
#> 56 NS 3
#> 57 15 1
#> 58 51 1
#> 59 72 1
#> 60 60 0
#> 61 66 0
#> 62 69 0
#> 63 78 0
#> 64 NB 0
#> 65 NL 0
#> 66 NT 0
#> 67 NU 0
#> 68 PE 0
#> 69 YT 0
#>
#>
#> $facets$facet_dates
#> NULL
#>
#> $facets$facet_ranges
#> NULL
#>
#>
#> attr(,"class")
#> [1] "bison_solr"
Highlighting
bison_solr(scientificName='Helianthus annuus', rows=1, hl='true',
hl.fl='scientificName')
#> $num_found
#> [1] 5982
#>
#> $points
#> eventDate providedScientificName year countryCode providedCounty
#> 1 2000-06-23T02:00Z Helianthus annuus L. 2000 US Colusa
#> ambiguous verbatimLocality latlon computedCountyFips
#> 1 FALSE -122.36707,39.01127 06011
#> occurrenceID decimalLongitude basisOfRecord providedCommonName
#> 1 1021808881 -122.3671 specimen
#> collectionID ownerInstitutionCollectionCode
#> 1 http://ucjeps.berkeley.edu/consortium/ Consortium of California Herbaria
#> scientificName computedStateFips license TSNs providerID
#> 1 Helianthus annuus 06 CC_BY_NC_4_0 36616 319
#> stateProvince higherGeographyID verbatimEventDate decimalLatitude
#> 1 California 06 23 2000 39.01127
#> coordinatePrecision verbatimElevation recordedBy
#> 1 310 m. Craig D. Thomsen
#> geo provider calculatedCounty
#> 1 -122.36707 39.01127 Consortium of California Herbaria Colusa County
#> verbatimDepth catalogNumber ITISscientificName
#> 1 UCD64431 Helianthus annuus
#> coordinateUncertaintyInMeters pointPath kingdom
#> 1 /-122.36707,39.01127/specimen Plantae
#> calculatedState
#> 1 California
#> hierarchy_homonym_string
#> 1 -202422-954898-846494-954900-846496-846504-18063-846535-35419-35420-36611-36616-
#> collectorNumber resourceID ITIStsn
#> 1 2428 319,202797 36616
#>
#> $highlight
#> $highlight$`1021808881`
#> $highlight$`1021808881`$scientificName
#> $highlight$`1021808881`$scientificName[[1]]
#> [1] "<em>Helianthus annuus</em>"
#>
#>
#>
#>
#> $facets
#> $facets$facet_queries
#> NULL
#>
#> $facets$facet_fields
#> NULL
#>
#> $facets$facet_dates
#> NULL
#>
#> $facets$facet_ranges
#> NULL
#>
#>
#> attr(,"class")
#> [1] "bison_solr"