Wrapper to the USGS Bison API
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README.md

rbison

Build Status Build status codecov.io rstudio mirror downloads cran version

Wrapper for the USGS Bison API.

Info

See https://bison.usgs.gov/#api for API docs for the BISON API.

Installation

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.

get data

out <- bison(species = "Phocoenoides dalli dalli", count = 10)

inspect summary

out$summary
#>   total specimen
#> 1     7        7

map occurrences

bisonmap(out)

plot of chunk unnamed-chunk-7

All points within the US (including AK and HI)

get data

out <- bison(species = "Bison bison", count = 600)

inspect summary

out$summary
#>   total observation fossil specimen unknown centroid
#> 1  1217         252    162      796       7        1

map occurrences

bisonmap(out)

plot of chunk unnamed-chunk-10

All points within the contiguous 48 states

get data

out <- bison(species = "Aquila chrysaetos", count = 600)

inspect summary

out$summary
#>   total observation fossil specimen literature unknown centroid
#> 1 91482       80582    118      785        556    9441        1

map occurrences

bisonmap(out)

plot of chunk unnamed-chunk-13

Map county or state level data

Counties - using last data call for Aquila

bisonmap(out, tomap = "county")

plot of chunk unnamed-chunk-14

States - using last data call for Aquila

bisonmap(out, tomap = "state")

plot of chunk unnamed-chunk-15

BISON SOLR interface

taxa

The taxa service searches for and gives back taxonomic names

bison_tax(query = "*bear")
#> $numFound
#> [1] 12
#> 
#> $names
#>       lc_vernacularName       vernacularName
#> 1   American black bear  American black bear
#> 2    Asiatic black bear   Asiatic black bear
#> 3     banded woollybear    banded woollybear
#> 4            black bear           black bear
#> 5      black-ended bear     black-ended bear
#> 6            brown bear           brown bear
#> 7          grizzly bear         grizzly bear
#> 8           Kodiak bear          Kodiak bear
#> 9  Louisiana black bear Louisiana black bear
#> 10             Sun bear             Sun bear
#> 
#> $highlight
#> NULL
#> 
#> $facets
#> NULL

And you can search by scientific name

bison_tax(query = "Helianthus*", method = "scientificName")
#> $numFound
#> [1] 215
#> 
#> $names
#>                       scientificName
#> 1  Helianthus divaricatus latifolius
#> 2             Helianthus decapetalus
#> 3                Helianthus ambiguus
#> 4             Helianthus dowellianus
#> 5               Helianthus luxurians
#> 6               Helianthus anomalus 
#> 7            Helianthus longifolius 
#> 8               Helianthus arenicola
#> 9                Helianthus parishii
#> 10             Helianthus floridanus
#> 
#> $highlight
#> NULL
#> 
#> $facets
#> NULL

occurrence search

The 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

bison_solr(scientificName = "Ursus americanus", state_code = "New Mexico", rows = 50, fl = "eventDate,scientificName")
#> $num_found
#> [1] 4801
#> 
#> $points
#>            eventDate   scientificName
#> 1  1995-05-28T00:00Z Ursus americanus
#> 2               <NA> Ursus americanus
#> 3  1973-09-19T00:00Z Ursus americanus
#> 4  1988-06-26T00:00Z Ursus americanus
#> 5  2012-09-24T00:00Z Ursus americanus
#> 6  2015-05-05T00:00Z Ursus americanus
#> 7  1996-05-28T00:00Z Ursus americanus
#> 8  2013-11-25T00:00Z Ursus americanus
#> 9               <NA> Ursus americanus
#> 10              <NA> Ursus americanus
#> 11              <NA> Ursus americanus
#> 12              <NA> Ursus americanus
#> 13              <NA> Ursus americanus
#> 14 2009-06-07T00:00Z Ursus americanus
#> 15 1958-09-11T00:00Z Ursus americanus
#> 16 1951-10-14T00:00Z Ursus americanus
#> 17              <NA> Ursus americanus
#> 18              <NA> Ursus americanus
#> 19              <NA> Ursus americanus
#> 20              <NA> Ursus americanus
#> 21              <NA> Ursus americanus
#> 22              <NA> Ursus americanus
#> 23              <NA> Ursus americanus
#> 24              <NA> Ursus americanus
#> 25              <NA> Ursus americanus
#> 26 2012-10-27T00:00Z Ursus americanus
#> 27 1955-08-27T00:00Z Ursus americanus
#> 28 1950-09-04T00:00Z Ursus americanus
#> 29 1954-12-28T00:00Z Ursus americanus
#> 30 1955-08-27T00:00Z Ursus americanus
#> 31 1954-10-13T00:00Z Ursus americanus
#> 32 1953-10-22T00:00Z Ursus americanus
#> 33 1957-01-14T00:00Z Ursus americanus
#> 34 1953-10-15T00:00Z Ursus americanus
#> 35 1954-11-12T00:00Z Ursus americanus
#> 36 1955-03-01T00:00Z Ursus americanus
#> 37 1956-05-24T00:00Z Ursus americanus
#> 38 1958-06-06T00:00Z Ursus americanus
#> 39 1958-08-27T00:00Z Ursus americanus
#> 40 1967-06-13T00:00Z Ursus americanus
#> 41              <NA> Ursus americanus
#> 42 2012-05-30T16:38Z Ursus americanus
#> 43              <NA> Ursus americanus
#> 44 2012-08-30T00:00Z Ursus americanus
#> 45 1995-11-25T00:00Z Ursus americanus
#> 46              <NA> Ursus americanus
#> 47              <NA> Ursus americanus
#> 48              <NA> Ursus americanus
#> 49 2015-06-04T00:00Z Ursus americanus
#> 50 1931-10-21T00:00Z 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"

Mapping the data

out <- bison_solr(scientificName = "Ursus americanus", rows = 200)
bisonmap(out)

plot of chunk unnamed-chunk-19

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rbison in R doing citation(package = 'rbison')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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.

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