Other functions available in rbison

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.

Load rbison

library('rbison')

Data provider statistics

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)

Data provider information

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

The Solr taxonomic name endpoint

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

The solr occurrence data endpoint

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"