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] "Kenelm W. Philip lepidoptera collection"
#> [5] "KNWR Entomology Collection"
#> [6] "KNWR Herbarium 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"
#>
#> $data
#> currentWeekTotals providerId resourceId lastUpdated todayTotals
#> 1 0 177 177,973 NA 0
#> 2 0 177 177,988 NA 0
#> 3 5618 177 177,13472 NA 759
#> 4 4724 177 177,976 NA 697
#> 5 5022 177 177,13468 NA 759
#> 6 4371 177 177,13474 NA 697
#> 7 0 177 177,972 NA 0
#> 8 4299 177 177,971 NA 697
#> 9 4299 177 177,14394 NA 697
#> janTotals yesterdayTotals lastWeekTotals febTotals marTotals aprTotals
#> 1 0 0 0 0 0 0
#> 2 0 0 0 0 0 0
#> 3 5810 759 2216 6855 12339 12915
#> 4 3816 697 1561 3357 7581 7751
#> 5 4888 759 1723 4598 10936 9347
#> 6 4862 697 1633 3989 8561 8449
#> 7 0 0 0 0 0 0
#> 8 3562 697 1597 3315 7432 10348
#> 9 3356 697 1561 3357 7565 7419
#> mayTotals junTotals julTotals augTotals sepTotals octTotals novTotals
#> 1 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0
#> 3 3556 0 0 0 0 0 0
#> 4 2871 0 0 0 0 0 0
#> 5 3061 0 0 0 0 0 0
#> 6 2710 0 0 0 0 0 0
#> 7 0 0 0 0 0 0 0
#> 8 2638 0 0 0 0 0 0
#> 9 2638 0 0 0 0 0 0
#> decTotals currentMonthTotals id type
#> 1 0 0 NA wms
#> 2 0 0 NA wms
#> 3 0 3556 NA wms
#> 4 0 2871 NA wms
#> 5 0 3061 NA wms
#> 6 0 2710 NA wms
#> 7 0 0 NA wms
#> 8 0 2638 NA wms
#> 9 0 2638 NA wms
out$Harvard_University_Herbaria
#> $name
#> [1] "Harvard University Herbaria"
#>
#> $resources
#> [1] "E.C. Smith Herbarium" "Harvard University Herbaria"
#>
#> $data
#> currentWeekTotals providerId resourceId lastUpdated todayTotals
#> 1 0 214 214,1829 NA 0
#> 2 7303 214 214,202435 NA 759
#> janTotals yesterdayTotals lastWeekTotals febTotals marTotals aprTotals
#> 1 0 0 0 0 0 0
#> 2 11305 759 6602 15384 19847 24486
#> mayTotals junTotals julTotals augTotals sepTotals octTotals novTotals
#> 1 0 0 0 0 0 0 0
#> 2 3750 0 0 0 0 0 0
#> decTotals currentMonthTotals id type
#> 1 0 0 NA wms
#> 2 0 3750 NA wms
out$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"
#>
#> $data
#> currentWeekTotals providerId resourceId lastUpdated todayTotals
#> 1 4259 300 300,15002 NA 697
#> 2 4324 300 300,201848 NA 697
#> 3 5171 300 300,202310 NA 697
#> 4 1727 300 300,13716 NA 21
#> janTotals yesterdayTotals lastWeekTotals febTotals marTotals aprTotals
#> 1 3476 697 1561 3343 7620 7913
#> 2 3479 697 1409 3927 8451 8149
#> 3 6573 697 1949 8765 13111 10918
#> 4 3300 21 1409 3314 7339 7267
#> mayTotals junTotals julTotals augTotals sepTotals octTotals novTotals
#> 1 2598 0 0 0 0 0 0
#> 2 2663 0 0 0 0 0 0
#> 3 3465 0 0 0 0 0 0
#> 4 66 0 0 0 0 0 0
#> decTotals currentMonthTotals id type
#> 1 0 2598 NA wms
#> 2 0 2663 NA wms
#> 3 0 3465 NA wms
#> 4 0 66 NA wms
head(bison_providers(provider_no=131))
#> id
#> 1 131
#> 2 131,11420
#> 3 131,595
#> 4 131,202619
#> 5 131,14537
#> 6 131,14526
#> name
#> 1 http //www.kahaku.go.jp/english/ National Museum of Nature and Science, Japan
#> 2 Akita Prefectural Museum Hiroki Watanabe Collection of mollusca
#> 3 Algae Collection of National Museum of Nature and Science
#> 4 Annelida collection of National Museum of Nature and Science
#> 5 Arthropoda Collection of the Seto Marine Biological Laboratory, Kyoto University
#> 6 Bacteria Collection of the Seto Marine Biological Laboratory, Kyoto University
out <- bison_providers(details=TRUE)
out$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] 54
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 American black bear American black bear
#> 2 American Black Bear American Black Bear
#> 3 Asian Black Bear Asian Black Bear
#> 4 Asiatic black bear Asiatic black bear
#> 5 banded woollybear banded woollybear
#> 6 Bear Canyon talussnail Bear Canyon talussnail
#> 7 Bear Creek slitmouth Bear Creek slitmouth
#> 8 bear daisy bear daisy
#> 9 bear flower bear flower
#> 10 bear garlic bear garlic
#>
#> $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] 54
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 American black bear American black bear
#> 2 American Black Bear American Black Bear
#> 3 Asian Black Bear Asian Black Bear
#> 4 Asiatic black bear Asiatic black bear
#> 5 banded woollybear banded woollybear
#> 6 Bear Canyon talussnail Bear Canyon talussnail
#> 7 Bear Creek slitmouth Bear Creek slitmouth
#> 8 bear daisy bear daisy
#> 9 bear flower bear flower
#> 10 bear garlic bear garlic
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
bison_tax(query="*bear", exact=TRUE)
#> $numFound
#> [1] 49
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 bear daisy bear daisy
#> 2 bear flower bear flower
#> 3 bear garlic bear garlic
#> 4 bear gum bear gum
#> 5 bear huckleberry bear huckleberry
#> 6 bear oak bear oak
#> 7 bear sedge bear sedge
#> 8 bear tupelo bear tupelo
#> 9 black bear black bear
#> 10 brown bear brown bear
#>
#> $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] 54
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 American black bear American black bear
#> 2 American Black Bear American Black Bear
#> 3 Asian Black Bear Asian Black Bear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
Return certain fields
bison_tax(query="*bear", method="vernacularName", fl='vernacularName')
#> $numFound
#> [1] 54
#>
#> $names
#> vernacularName
#> 1 American black bear
#> 2 American Black Bear
#> 3 Asian Black Bear
#> 4 Asiatic black bear
#> 5 banded woollybear
#> 6 Bear Canyon talussnail
#> 7 Bear Creek slitmouth
#> 8 bear daisy
#> 9 bear flower
#> 10 bear garlic
#>
#> $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] 2464
#>
#> $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] 2464
#>
#> $points
#> decimalLongitude scientificName decimalLatitude
#> 1 -130.0534 Ursus americanus 55.97687
#> 2 -135.8470 Ursus americanus 58.47447
#> 3 -134.5484 Ursus americanus 58.41618
#>
#> $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)$points[,1:6]
#> providedScientificName countryCode providedCounty ambiguous
#> 1 Pelecaniformes US Polk FALSE
#> 2 Pelecaniformes US <NA> FALSE
#> verbatimLocality latlon
#> 1 PEACE RIVER MINE -81.77,27.8
#> 2 <NA> -119.7,34.4
bison_solr(kingdom = "Plantae", rows=2)$points[,1:6]
#> eventDate providedScientificName year countryCode
#> 1 2017-05-13 Papaver heterophyllum (Benth.) Greene 2017 US
#> 2 2017-05-13 Quercus velutina Lam. 2017 US
#> ambiguous latlon
#> 1 FALSE -121.911625,37.884973
#> 2 FALSE -82.018411,34.147879
Using additional solr fields - Faceting
bison_solr(scientificName='Helianthus annuus', rows=0, facet='true',
facet.field='computedStateFips')
#> $num_found
#> [1] 10442
#>
#> $points
#> NULL
#>
#> $highlight
#> NULL
#>
#> $facets
#> $facets$facet_queries
#> NULL
#>
#> $facets$facet_fields
#> $facets$facet_fields$computedStateFips
#> X1 X2
#> 1 06 2444
#> 2 48 1336
#> 3 08 568
#> 4 20 496
#> 5 35 440
#> 6 04 359
#> 7 46 292
#> 8 30 233
#> 9 49 230
#> 10 31 211
#> 11 16 206
#> 12 29 186
#> 13 41 178
#> 14 38 164
#> 15 56 163
#> 16 53 148
#> 17 17 138
#> 18 32 130
#> 19 40 121
#> 20 19 78
#> 21 25 61
#> 22 12 54
#> 23 22 54
#> 24 26 49
#> 25 SK 48
#> 26 39 43
#> 27 55 41
#> 28 05 40
#> 29 27 40
#> 30 36 40
#> 31 09 38
#> 32 47 37
#> 33 37 35
#> 34 AB 34
#> 35 18 33
#> 36 23 33
#> 37 BC 31
#> 38 21 28
#> 39 42 25
#> 40 45 23
#> 41 34 22
#> 42 54 21
#> 43 33 18
#> 44 24 17
#> 45 ON 17
#> 46 50 15
#> 47 MB 14
#> 48 02 11
#> 49 28 11
#> 50 13 9
#> 51 11 7
#> 52 44 7
#> 53 01 6
#> 54 15 6
#> 55 NS 5
#> 56 10 4
#> 57 51 4
#> 58 NB 4
#> 59 QC 4
#> 60 72 1
#> 61 60 0
#> 62 66 0
#> 63 69 0
#> 64 78 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] 10442
#>
#> $points
#> establishmentMeans eventDate providedScientificName year countryCode
#> 1 AK HI 2017-05-14 Helianthus annuus L. 2017 US
#> ambiguous latlon computedCountyFips occurrenceID
#> 1 FALSE -97.10123,32.583984 48439 1562942729
#> decimalLongitude basisOfRecord collectionID
#> 1 -97.10123 observation http://www.inaturalist.org/observations
#> ownerInstitutionCollectionCode scientificName
#> 1 iNaturalist Research-grade Observations Helianthus annuus
#> institutionID computedStateFips license TSNs
#> 1 http://www.inaturalist.org 48 CC_BY_NC_4_0 36616
#> providerID decimalLatitude recordedBy geo
#> 1 407 32.58398 Bob O'Kennon -97.10123 32.583984
#> provider calculatedCounty catalogNumber ITISscientificName
#> 1 iNaturalist.org Tarrant 6228598 Helianthus annuus
#> pointPath kingdom calculatedState
#> 1 /-97.10123,32.583984/observation Plantae Texas
#> hierarchy_homonym_string
#> 1 -202422-954898-846494-954900-846496-846504-18063-846535-35419-35420-36611-36616-
#> ITIScommonName resourceID
#> 1 annual sunflower;common sunflower;sunflower;wild sunflower 407,202485
#> ITIStsn
#> 1 36616
#>
#> $highlight
#> $highlight$`1562942729`
#> $highlight$`1562942729`$scientificName
#> $highlight$`1562942729`$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"