Wrapper for the USGS Bison API
USGS Biodiversity Information Serving Our Nation (BISON) is a web-based federal mapping resource that provides access to georeferenced (those with latitude and longitude coordinates) and non-georeferenced data describing the occurrence or presence of terrestrial and aquatic species recorded or collected by a person (or instrument) at a specific time in the United States and its Territories. Each record in a species occurrence dataset available in BISON will typically consist of a scientific name (genus and specific epithet), a date, and one or more geographic references such as a state name, county name, and/or decimal latitude and longitude coordinates. In addition to these typical data fields, species occurrence datasets often include many other data fields that describe each species occurrence event in more detail.
rbison allows one to pull species occurrence data from these datasets, inspect species occurance summaries, and then map species occurance within the US, within the contiguous 48 states, and/or at county or state level.
Current data providers for BISON can be found at https://bison.usgs.gov/providers.jsp
See https://bison.usgs.gov/#api for API docs for the BISON API.
From CRAN
install.packages("rbison")Or the development version from Github
install.packages("devtools")
devtools::install_github("ropensci/rbison")
library('rbison')Load package
library("rbison")Notice that the function bisonmap automagically selects the map extent to plot for you, being one of the contiguous lower 48 states, or the lower 48 plus AK and HI, or a global map. If some or all points outside the US, a global map is drawn, and throws a warning. . You may want to make sure the occurrence lat/long coordinates are correct.
out <- bison(species = "Phocoenoides dalli dalli", count = 10)out$summary
#> specimen specimen.1
#> 1 7 7bisonmap(out)
out <- bison(species = "Bison bison", count = 300)out$summary
#> occurrences.legend.fossil occurrences.legend.observation
#> 1 359 927
#> occurrences.legend.centroid occurrences.legend.specimen
#> 1 1 946
#> occurrences.legend.unknown fossil observation centroid specimen unknown
#> 1 6 359 927 1 946 6bisonmap(out)
out <- bison(species = "Aquila chrysaetos", count = 300)out$summary
#> occurrences.legend.literature occurrences.legend.fossil
#> 1 1641 642
#> occurrences.legend.observation occurrences.legend.centroid
#> 1 128207 1
#> occurrences.legend.unknown occurrences.legend.specimen literature fossil
#> 1 9734 1899 1641 642
#> observation centroid unknown specimen
#> 1 128207 1 9734 1899bisonmap(out)
bisonmap(out, tomap = "county")
bisonmap(out, tomap = "state")
The taxa service searches for and gives back taxonomic names
bison_tax(query = "*bear")
#> $numFound
#> [1] 48
#>
#> $names
#> lc_vernacularName vernacularName
#> 1 Louisiana black bear Louisiana black bear
#> 2 Sloth Bear Sloth Bear
#> 3 grizzly bear grizzly bear
#> 4 bear oak bear oak
#> 5 yellow woollybear yellow woollybear
#> 6 bear daisy bear daisy
#> 7 banded woollybear banded woollybear
#> 8 Asiatic black bear Asiatic black bear
#> 9 Kodiak bear Kodiak bear
#> 10 black-ended bear black-ended bear
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULLAnd you can search by scientific name
bison_tax(query = "Helianthus*", method = "scientificName")
#> $numFound
#> [1] 212
#>
#> $names
#> scientificName
#> 1 Discoaster helianthus
#> 2 Helianthus divaricatus latifolius
#> 3 Helianthus decapetalus
#> 4 Helianthus ambiguus
#> 5 Helianthus dowellianus
#> 6 Helianthus luxurians
#> 7 Helianthus arenicola
#> 8 Helianthus atrorubens
#> 9 Helianthus frondosus
#> 10 Helianthus nuttallii canadensis
#>
#> $highlight
#> NULL
#>
#> $facets
#> NULLThe occurrence service searches by scientific names and gives back occurrence data similar to data given back by the bison() function
Searching for data and looking at output
x <- bison_solr(scientificName = "Ursus americanus", rows = 10,
fl = "scientificName,decimalLongitude,decimalLatitude")
x$points
#> decimalLongitude scientificName decimalLatitude
#> 1 -92.8370 Ursus americanus 48.48344
#> 2 -150.5500 Ursus americanus 59.59000
#> 3 -150.5500 Ursus americanus 59.59000
#> 4 -149.6600 Ursus americanus 59.83000
#> 5 -124.0676 Ursus americanus 46.28618
#> 6 -121.5178 Ursus americanus 41.75872
#> 7 -143.4417 Ursus americanus 64.95393
#> 8 -109.6747 Ursus americanus 34.98864
#> 9 -123.4106 Ursus americanus 47.78021
#> 10 -116.1590 Ursus americanus 33.98085Mapping the data
out <- bison_solr(scientificName = "Ursus americanus", rows = 200)
bisonmap(out)
rbison in R doing citation(package = 'rbison')This package is part of a richer suite called SPOCC Species Occurrence Data, along with several other packages, that provide access to occurrence records from multiple databases. We recommend using SPOCC as the primary R interface to rbison unless your needs are limited to this single source.
