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] "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

Data provider information

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

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] 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

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='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"