rbison v1.0.0

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Interface to the 'USGS' 'BISON' API

Interface to the 'USGS' 'BISON' (<https://bison.usgs.gov/>) API, a 'database' for species occurrence data. Data comes from species in the United States from participating data providers. You can get data via 'taxonomic' and location based queries. A simple function is provided to help visualize data.

Readme

rbison

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Wrapper for the USGS Bison (https://bison.usgs.gov) API

Description

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, U.S. Territories, U.S. Marine Exclusive Economic Zones (EEZs), and Canada. 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.

BISON is the US Node of GBIF and regularly updates from GBIF to have full coverage and is committed to eventually providing most BISON originating data to GBIF, however, users should be aware that several million BISON records are not in GBIF. The Solr API for BISON is fully open with no limits, allowing full batch download, faceting and geospatial searches on both DC fields and BISON added fields such as the full ITIS taxonomy, FIPS Codes, and georeferencing of county records to documented centroids.

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/doc/api.jsp for API docs for the BISON API.

Installation

From CRAN

install.packages("rbison")

Or the development version from Github

remotes::install_github("ropensci/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
#> $specimen
#> [1] 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 = "Cyanocitta stelleri", count = 500)

inspect summary

out$summary
#> $fossil
#> [1] 4
#> 
#> $observation
#> [1] 712380
#> 
#> $centroid
#> [1] 1
#> 
#> $specimen
#> [1] 3438
#> 
#> $unknown
#> [1] 208

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 = 300)

inspect summary

out$summary
#> $fossil
#> [1] 681
#> 
#> $observation
#> [1] 159076
#> 
#> $centroid
#> [1] 1
#> 
#> $unknown
#> [1] 11046
#> 
#> $specimen
#> [1] 1911

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")

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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] 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

And you can search by scientific name

bison_tax(query = "Helianthus*", method = "scientificName")
#> $numFound
#> [1] 240
#> 
#> $names
#>                     scientificName
#> 1            Discoaster helianthus
#> 2           Helianthus decapetalus
#> 3              Helianthus ambiguus
#> 4          Helianthus crassifolius
#> 5           Helianthus dowellianus
#> 6             Helianthus luxurians
#> 7             Helianthus arenicola
#> 8            Helianthus atrorubens
#> 9             Helianthus frondosus
#> 10 Helianthus nuttallii canadensis
#> 
#> $highlight
#> NULL
#> 
#> $facets
#> NULL

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

x <- bison_solr(scientificName = "Aquila chrysaetos", rows = 10, 
    fl = "scientificName,decimalLongitude,decimalLatitude")
x$points
#>       scientificName
#> 1  Aquila chrysaetos
#> 2  Aquila chrysaetos
#> 3  Aquila chrysaetos
#> 4  Aquila chrysaetos
#> 5  Aquila chrysaetos
#> 6  Aquila chrysaetos
#> 7  Aquila chrysaetos
#> 8  Aquila chrysaetos
#> 9  Aquila chrysaetos
#> 10 Aquila chrysaetos

Mapping the data

out <- bison_solr(scientificName = "Aquila chrysaetos", rows = 1000)
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 (https://github.com/ropensci/spocc), 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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Functions in rbison

Name Description
bison_datause Get BISON data use agreement details and examples for how to cite data.
bison_solr Search for and collect occurrence data from the USGS Bison API using their solr endpoint.
fips Fips codes for states and counties
is.bison_solr Check if object is of class bison_solr
bisonmap Make map to visualize BISON data.
all_states Data for a states map
rbison-package rbison is an interface to the USGS Bison API.
bison_tax Search for and collect taxonomic name data from the USGS Bison API using solr
bison_providers Get information about BISON data providers.
bison_stats Get statistics about BISON downloads.
is.bison Check if object is of class bison
bison Search for and collect data from the USGS Bison API.
No Results!

Vignettes of rbison

Name
other_functions.Rmd
rbison.Rmd
No Results!

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Details

License MIT + file LICENSE
URL https://github.com/ropensci/rbison (devel) https://docs.ropensci.org/rbison (docs)
BugReports https://github.com/ropensci/rbison/issues
LazyData true
VignetteBuilder knitr
Encoding UTF-8
Language en-US
RoxygenNote 7.1.0
X-schema.org-applicationCategory DataAccess
X-schema.org-keywords species, occurrences, biodiversity, maps, USGS, BISON
X-schema.org-isPartOf "https://ropensci.org"
NeedsCompilation no
Packaged 2020-06-08 17:52:29 UTC; sckott
Repository CRAN
Date/Publication 2020-06-08 18:30:03 UTC

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