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"
#>
#> $data
#> Source: local data frame [9 x 22]
#>
#> todayTotals currentWeekTotals providerId resourceId lastUpdated
#> 1 228 3592 177 177,973 NA
#> 2 228 3446 177 177,988 NA
#> 3 335 3447 177 177,13472 NA
#> 4 308 3368 177 177,13468 NA
#> 5 284 3323 177 177,13474 NA
#> 6 0 0 177 177,976 NA
#> 7 302 3694 177 177,972 NA
#> 8 228 3239 177 177,971 NA
#> 9 329 3541 177 177,14394 NA
#> Variables not shown: yesterdayTotals (int), lastWeekTotals (int),
#> janTotals (int), febTotals (int), marTotals (int), aprTotals (int),
#> mayTotals (int), junTotals (int), julTotals (int), augTotals (int),
#> sepTotals (int), octTotals (int), novTotals (int), decTotals (int),
#> currentMonthTotals (int), id (lgl), type (chr)
out$Harvard_University_Herbaria
#> $name
#> [1] "Harvard University Herbaria"
#>
#> $resources
#> [1] "E.C. Smith Herbarium" "Harvard University Herbaria"
#>
#> $data
#> Source: local data frame [2 x 22]
#>
#> todayTotals currentWeekTotals providerId resourceId lastUpdated
#> 1 0 0 214 214,1829 NA
#> 2 518 4272 214 214,1827 NA
#> Variables not shown: yesterdayTotals (int), lastWeekTotals (int),
#> janTotals (int), febTotals (int), marTotals (int), aprTotals (int),
#> mayTotals (int), junTotals (int), julTotals (int), augTotals (int),
#> sepTotals (int), octTotals (int), novTotals (int), decTotals (int),
#> currentMonthTotals (int), id (lgl), type (chr)
out$ZooKeys
#> $name
#> [1] "ZooKeys"
#>
#> $resources
#> [1] "Localities for the arachnid genus Acuclavella (Opiliones, Ceratolasmatidae)"
#> [2] "Megophthalmidia_of_North_America"
#> [3] "Western Palaearctic Ectoedemia (Zimmermannia) Hering and Ectoedemia Busck s. str. (Lepidoptera: Nepticulidae): five new species and new data on distribution, hostplants and recognition"
#>
#> $data
#> Source: local data frame [3 x 22]
#>
#> todayTotals currentWeekTotals providerId resourceId lastUpdated
#> 1 284 3323 300 300,15002 NA
#> 2 228 3239 300 300,200009 NA
#> 3 0 0 300 300,13716 NA
#> Variables not shown: yesterdayTotals (int), lastWeekTotals (int),
#> janTotals (int), febTotals (int), marTotals (int), aprTotals (int),
#> mayTotals (int), junTotals (int), julTotals (int), augTotals (int),
#> sepTotals (int), octTotals (int), novTotals (int), decTotals (int),
#> currentMonthTotals (int), id (lgl), type (chr)
head(bison_providers(provider_no=131))
#> id
#> 1 131
#> 2 131,11420
#> 3 131,595
#> 4 131,200040
#> 5 131,14537
#> 6 131,14526
#> name
#> 1 http //www.kahaku.go.jp/english/ National Museum of Nature and Science, Japan
#> 2 Akita Prefectural Museum Hiroki Watanabe Collection of mollusca
#> 3 Algae Collection of National Museum of Nature and Science
#> 4 Annelida collection of National Museum of Nature and Science
#> 5 Arthropoda Collection of the Seto Marine Biological Laboratory, Kyoto University
#> 6 Bacteria Collection of the Seto Marine Biological Laboratory, Kyoto University
out <- bison_providers(details=TRUE)
out$National_Herbarium_of_New_South_Wales
#> provider_name
#> 1 National Herbarium of New South Wales
#> 2 National Herbarium of New South Wales
#> provider_url id
#> 1 http://bison.usgs.ornl.gov/api/providers/details 126,968
#> 2 http://bison.usgs.ornl.gov/api/providers/details 126,969
#> name url
#> 1 NSW herbarium collection http://plantnet.rbgsyd.nsw.gov.au
#> 2 Plants of Papua New Guinea 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] 12
#>
#> $names
#> Source: local data frame [10 x 2]
#>
#> vernacularName lc_vernacularName
#> 1 Louisiana black bear Louisiana black bear
#> 2 grizzly bear grizzly bear
#> 3 yellow woollybear yellow woollybear
#> 4 banded woollybear banded woollybear
#> 5 Asiatic black bear Asiatic black bear
#> 6 Kodiak bear Kodiak bear
#> 7 black-ended bear black-ended bear
#> 8 American black bear American black bear
#> 9 black bear black bear
#> 10 yellow woolly bear yellow woolly 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] 12
#>
#> $names
#> Source: local data frame [10 x 2]
#>
#> vernacularName lc_vernacularName
#> 1 Louisiana black bear Louisiana black bear
#> 2 grizzly bear grizzly bear
#> 3 yellow woollybear yellow woollybear
#> 4 banded woollybear banded woollybear
#> 5 Asiatic black bear Asiatic black bear
#> 6 Kodiak bear Kodiak bear
#> 7 black-ended bear black-ended bear
#> 8 American black bear American black bear
#> 9 black bear black bear
#> 10 yellow woolly bear yellow woolly bear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
bison_tax(query="*bear", exact=TRUE)
#> $numFound
#> [1] 0
#>
#> $names
#> Source: local data frame [0 x 0]
#>
#>
#> $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] 12
#>
#> $names
#> Source: local data frame [3 x 2]
#>
#> vernacularName lc_vernacularName
#> 1 Louisiana black bear Louisiana black bear
#> 2 grizzly bear grizzly bear
#> 3 yellow woollybear yellow woollybear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULL
Return certain fields
bison_tax(query="*bear", method="vernacularName", fl='vernacularName')
#> $numFound
#> [1] 12
#>
#> $names
#> Source: local data frame [10 x 1]
#>
#> vernacularName
#> 1 Louisiana black bear
#> 2 grizzly bear
#> 3 yellow woollybear
#> 4 banded woollybear
#> 5 Asiatic black bear
#> 6 Kodiak bear
#> 7 black-ended bear
#> 8 American black bear
#> 9 black bear
#> 10 yellow woolly 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='New Mexico',
fl="scientificName", rows=3)
#> $num_found
#> [1] 5370
#>
#> $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='New Mexico',
rows=3, fl="eventDate,scientificName")
#> $num_found
#> [1] 5370
#>
#> $points
#> eventDate scientificName
#> 1 2012-05-19T00:00Z Ursus americanus
#> 2 2012-06-23T00:00Z Ursus americanus
#> 3 2009-10-17T14:54Z 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(TSNs = 174670, rows=2)$points[,1:6]
#> computedCountyFips providerID catalogNumber basisOfRecord countryCode
#> 1 12071 407 504817 observation US
#> 2 12001 407 1040366 observation US
#> ITISscientificName
#> 1 Pelecaniformes
#> 2 Pelecaniformes
bison_solr(kingdom = "Plantae", rows=2)$points[,1:6]
#> computedCountyFips providerID catalogNumber basisOfRecord countryCode
#> 1 41029 25 4495 specimen US
#> 2 41033 141 OSC23124 specimen US
#> ITISscientificName
#> 1 Isothecium myosuroides
#> 2 Luzula parviflora
Using additional solr fields - Faceting
bison_solr(scientificName='Helianthus annuus', rows=0, facet='true',
facet.field='computedStateFips')
#> $num_found
#> [1] 5365
#>
#> $points
#> NULL
#>
#> $highlight
#> NULL
#>
#> $facets
#> $facets$facet_queries
#> NULL
#>
#> $facets$facet_fields
#> $facets$facet_fields$computedStateFips
#> X1 X2
#> 1 06 1272
#> 2 20 369
#> 3 48 362
#> 4 35 311
#> 5 08 277
#> 6 04 250
#> 7 46 127
#> 8 29 116
#> 9 30 107
#> 10 31 102
#> 11 49 91
#> 12 17 85
#> 13 38 79
#> 14 40 77
#> 15 16 75
#> 16 41 75
#> 17 56 68
#> 18 53 61
#> 19 19 44
#> 20 26 42
#> 21 32 37
#> 22 05 33
#> 23 09 31
#> 24 22 31
#> 25 25 28
#> 26 39 28
#> 27 27 26
#> 28 47 25
#> 29 21 21
#> 30 12 20
#> 31 18 20
#> 32 42 19
#> 33 37 18
#> 34 36 15
#> 35 45 13
#> 36 34 11
#> 37 54 10
#> 38 23 9
#> 39 55 8
#> 40 24 6
#> 41 28 6
#> 42 01 5
#> 43 13 5
#> 44 33 5
#> 45 44 5
#> 46 50 5
#> 47 02 4
#> 48 11 4
#> 49 15 2
#> 50 51 2
#> 51 10 1
#> 52 60 0
#> 53 66 0
#> 54 69 0
#> 55 72 0
#> 56 78 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] 5365
#>
#> $points
#> computedCountyFips providerID catalogNumber basisOfRecord countryCode
#> 1 25015 266 CONN00026678 specimen US
#> ITISscientificName latlon calculatedState decimalLongitude
#> 1 Helianthus annuus -72.51666,42.36666 Massachusetts -72.51666
#> year ITIStsn
#> 1 1885 36616
#> hierarchy_homonym_string
#> 1 -202422-954898-846494-954900-846496-846504-18063-846535-35419-35420-36611-36616-
#> geo TSNs calculatedCounty pointPath
#> 1 -72.51666 42.36666 36616 Hampshire County /-72.51666,42.36666/specimen
#> computedStateFips providedCounty kingdom decimalLatitude
#> 1 25 Hampshire County Plantae 42.36666
#> collectionID occurrenceID recordedBy
#> 1 http://bgbaseserver.eeb.uconn.edu/ 415907013 Wm. M. Shepardson
#> providedScientificName ownerInstitutionCollectionCode
#> 1 Helianthus annuus L. CONN
#> provider ambiguous resourceID stateProvince
#> 1 University of Connecticut FALSE 266,13544 Massachusetts
#> ITIScommonName
#> 1 annual sunflower;common sunflower;sunflower;wild sunflower
#> scientificName institutionID
#> 1 Helianthus annuus http://bgbaseserver.eeb.uconn.edu/
#>
#> $highlight
#> $highlight$`415907013`
#> $highlight$`415907013`$scientificName
#> $highlight$`415907013`$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"