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"
#>
#> $data
#> Source: local data frame [9 x 22]
#>
#> id type providerId todayTotals currentWeekTotals resourceId lastUpdated
#> 1 NA wms 177 235 256 177,973 NA
#> 2 NA wms 177 77 98 177,988 NA
#> 3 NA wms 177 77 98 177,13472 NA
#> 4 NA wms 177 77 98 177,13468 NA
#> 5 NA wms 177 77 98 177,13474 NA
#> 6 NA wms 177 0 0 177,976 NA
#> 7 NA wms 177 109 130 177,972 NA
#> 8 NA wms 177 77 98 177,971 NA
#> 9 NA wms 177 77 98 177,14394 NA
#> Variables not shown: yesterdayTotals (int), lastWeekTotals (int),
#> janTotals (int), febTotals (int), marTotals (int), aprTotals (int),
#> mayTotals (int), junTotals (int), julTotals (int), augTotals (int),
#> sepTotals (int), octTotals (int), novTotals (int), decTotals (int),
#> currentMonthTotals (int)
out$Harvard_University_Herbaria
#> $name
#> [1] "Harvard University Herbaria"
#>
#> $resources
#> [1] "E.C. Smith Herbarium" "Harvard University Herbaria"
#>
#> $data
#> Source: local data frame [2 x 22]
#>
#> id type providerId todayTotals currentWeekTotals resourceId lastUpdated
#> 1 NA wms 214 0 0 214,1829 NA
#> 2 NA wms 214 188 490 214,1827 NA
#> Variables not shown: yesterdayTotals (int), lastWeekTotals (int),
#> janTotals (int), febTotals (int), marTotals (int), aprTotals (int),
#> mayTotals (int), junTotals (int), julTotals (int), augTotals (int),
#> sepTotals (int), octTotals (int), novTotals (int), decTotals (int),
#> currentMonthTotals (int)
out$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"
#>
#> $data
#> Source: local data frame [3 x 22]
#>
#> id type providerId todayTotals currentWeekTotals resourceId lastUpdated
#> 1 NA wms 300 77 98 300,15002 NA
#> 2 NA wms 300 77 109 300,200009 NA
#> 3 NA wms 300 0 0 300,13716 NA
#> Variables not shown: yesterdayTotals (int), lastWeekTotals (int),
#> janTotals (int), febTotals (int), marTotals (int), aprTotals (int),
#> mayTotals (int), junTotals (int), julTotals (int), augTotals (int),
#> sepTotals (int), octTotals (int), novTotals (int), decTotals (int),
#> currentMonthTotals (int)
head(bison_providers(provider_no=131))
#> id
#> 1 131
#> 2 131,11420
#> 3 131,595
#> 4 131,200040
#> 5 131,14537
#> 6 131,14526
#> name
#> 1 http //www.kahaku.go.jp/english/ National Museum of Nature and Science, Japan
#> 2 Akita Prefectural Museum Hiroki Watanabe Collection of mollusca
#> 3 Algae Collection of National Museum of Nature and Science
#> 4 Annelida collection of National Museum of Nature and Science
#> 5 Arthropoda Collection of the Seto Marine Biological Laboratory, Kyoto University
#> 6 Bacteria Collection of the Seto Marine Biological Laboratory, Kyoto University
out <- bison_providers(details=TRUE)
out$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 woolly bear yellow woolly bear
#> 4 American black bear American black bear
#> 5 black bear black bear
#> 6 Sun bear Sun bear
#> 7 yellow woollybear yellow woollybear
#> 8 banded woollybear banded woollybear
#> 9 Asiatic black bear Asiatic black bear
#> 10 Kodiak bear Kodiak 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 woolly bear yellow woolly bear
#> 4 American black bear American black bear
#> 5 black bear black bear
#> 6 Sun bear Sun bear
#> 7 yellow woollybear yellow woollybear
#> 8 banded woollybear banded woollybear
#> 9 Asiatic black bear Asiatic black bear
#> 10 Kodiak bear Kodiak 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 woolly bear yellow woolly bear
#>
#> $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 woolly bear
#> 4 American black bear
#> 5 black bear
#> 6 Sun bear
#> 7 yellow woollybear
#> 8 banded woollybear
#> 9 Asiatic black bear
#> 10 Kodiak 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] 5137
#>
#> $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] 5137
#>
#> $points
#> scientificName eventDate
#> 1 Ursus americanus <NA>
#> 2 Ursus americanus 1969-09-04T00:00Z
#> 3 Ursus americanus 1999-06-22T00:00Z
#>
#> $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)$points[,1:6]
#> computedCountyFips providerID catalogNumber basisOfRecord countryCode
#> 1 06079 407 240245 observation US
#> 2 06087 535 168878 fossil US
#> ITISscientificName
#> 1 Pelecaniformes
#> 2 Pelecaniformes
bison_solr(kingdom = "Plantae", rows=2)$points[,1:6]
#> providerID collectorNumber catalogNumber basisOfRecord countryCode
#> 1 220 3256 235754.10773092 unknown US
#> 2 114 <NA> 803 specimen US
#> ITISscientificName
#> 1 Argemone
#> 2 Argemone
Using additional solr fields - Faceting
bison_solr(scientificName='Helianthus annuus', rows=0, facet='true',
facet.field='computedStateFips')
#> $num_found
#> [1] 5108
#>
#> $points
#> NULL
#>
#> $highlight
#> NULL
#>
#> $facets
#> $facets$facet_queries
#> NULL
#>
#> $facets$facet_fields
#> $facets$facet_fields$computedStateFips
#> X1 X2
#> 1 06 1071
#> 2 20 329
#> 3 48 329
#> 4 35 296
#> 5 08 262
#> 6 04 156
#> 7 46 122
#> 8 29 115
#> 9 31 99
#> 10 17 84
#> 11 49 82
#> 12 30 79
#> 13 38 76
#> 14 41 74
#> 15 40 73
#> 16 16 68
#> 17 56 61
#> 18 53 60
#> 19 19 43
#> 20 26 35
#> 21 32 32
#> 22 09 31
#> 23 22 31
#> 24 05 30
#> 25 39 27
#> 26 27 25
#> 27 47 25
#> 28 25 22
#> 29 21 21
#> 30 12 19
#> 31 18 19
#> 32 42 19
#> 33 37 16
#> 34 36 13
#> 35 45 13
#> 36 34 10
#> 37 54 9
#> 38 23 8
#> 39 55 7
#> 40 01 5
#> 41 24 5
#> 42 33 5
#> 43 44 5
#> 44 02 4
#> 45 11 4
#> 46 13 4
#> 47 28 4
#> 48 50 4
#> 49 15 2
#> 50 10 1
#> 51 51 0
#> 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] 5108
#>
#> $points
#> computedCountyFips providerID catalogNumber basisOfRecord countryCode
#> 1 06041 319 UC1176903 specimen US
#> ITISscientificName latlon calculatedState
#> 1 Helianthus annuus -122.56939570846544,38.10733275261566 California
#> decimalLongitude year ITIStsn
#> 1 -122.6 1946 36616
#> hierarchy_homonym_string
#> 1 -202422-846492-846494-846496-846504-846505-18063-846535-35419-35420-36611-36616-
#> TSNs calculatedCounty pointPath
#> 1 36616 Marin County /-122.56939570846544,38.10733275261566/specimen
#> computedStateFips providedCounty kingdom decimalLatitude
#> 1 06 Marin Plantae 38.11
#> collectionID occurrenceID recordedBy
#> 1 http://ucjeps.berkeley.edu/consortium/ 868133992 John Thomas Howell
#> providedScientificName eventDate
#> 1 Helianthus annuus L. 1946-09-20T00:00Z
#> ownerInstitutionCollectionCode provider
#> 1 Consortium of California Herbaria Consortium of California Herbaria
#> ambiguous resourceID stateProvince
#> 1 FALSE 319,200079 California
#> ITIScommonName
#> 1 annual sunflower;common sunflower;sunflower;wild sunflower
#> scientificName
#> 1 Helianthus annuus
#>
#> $highlight
#> $highlight$`868133992`
#> $highlight$`868133992`$scientificName
#> $highlight$`868133992`$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"