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" 
#> 
#> $data
#> Source: local data frame [9 x 22]
#> 
#>   id type providerId todayTotals currentWeekTotals resourceId lastUpdated
#> 1 NA  wms        177         235               256    177,973          NA
#> 2 NA  wms        177          77                98    177,988          NA
#> 3 NA  wms        177          77                98  177,13472          NA
#> 4 NA  wms        177          77                98  177,13468          NA
#> 5 NA  wms        177          77                98  177,13474          NA
#> 6 NA  wms        177           0                 0    177,976          NA
#> 7 NA  wms        177         109               130    177,972          NA
#> 8 NA  wms        177          77                98    177,971          NA
#> 9 NA  wms        177          77                98  177,14394          NA
#> Variables not shown: yesterdayTotals (int), lastWeekTotals (int),
#>   janTotals (int), febTotals (int), marTotals (int), aprTotals (int),
#>   mayTotals (int), junTotals (int), julTotals (int), augTotals (int),
#>   sepTotals (int), octTotals (int), novTotals (int), decTotals (int),
#>   currentMonthTotals (int)
out$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)

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 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

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] 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"