Introduction to rbison

In rbison: Interface to the 'USGS' 'BISON' API

NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")
knitr::opts_chunk$set(
  fig.width = 6,
  fig.height = 4,
  comment = "#>",
  collapse = TRUE,
  warning = FALSE,
  message = FALSE,
  purl = NOT_CRAN,
  eval = NOT_CRAN
)

rbison is an R package to search and retrieve data from the USGS BISON service. rbison wraps R code around the BISON API to allow you to talk to the BISON database from R.

BISON has occurrence data for the US only.

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.

Info

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

Install rbison

install.packages("rbison")

Or install development version from Github

install.packages("devtools")
devtools::install_github("ropensci/rbison")

Load packages

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 = "Helianthus annuus", count = 10)

Inspect summary

out$summary

Map occurrences

head(out$counties)

All points within the US (including AK and HI)

Get data

out <- bison(species="Bison bison", count=200)

Inspect summary

out$summary

Map occurrences

bisonmap(out, tomap="state")

All points within the contiguous 48 states

Get data

out <- bison(species="Aquila chrysaetos", count=400)

Inspect summary

out$summary

Map occurrences

bisonmap(out, tomap="points")

Plot county or state

With any data returned from a bison call, you can choose to plot county or state level data

Counties - using last data call for Aquila

bisonmap(out, tomap="county")

States - using last data call for Aquila

bisonmap(out, tomap="state")

Constrain search with county IDs or bounding boxes

Constrain search to a certain county.

Check out https://en.wikipedia.org/wiki/Federal_Information_Processing_Standard_state_code to get state and county fips codes. Fips codes are like so: First two digits are the state code - last three are the county code. For example the 06 in 06037 is the state of California, and the 037 is the Los Angeles county.

out <- bison(species="Helianthus annuus", countyFips = "06037")

Inspect summary

out$summary

By default, the query only returned 10 records

head(out$points)

Or specify county by its actual name - probably much easier.

out <- bison(species="Helianthus annuus", county = "Los Angeles")

Inspect summary

out$summary

By default, the query only returned 10 records

head(out$points)

bison will help you if you spell the name wrong, or use a partial name. The results are not printed below, but you would get a prompt asking you to pick between the two counties that start with Los.

bison(species="Helianthus annuus", county = "Los")

Constrain search to a amorphous area.

Check out http://en.wikipedia.org/wiki/Well-known_text for an in depth look at the options, terminology, etc.

out <- bison(species="Helianthus annuus", aoi = "POLYGON((-111.06360117772908 38.84001566645886,-110.80542246679359 39.37707771107983,-110.20117441992392 39.17722368276862,-110.20666758398464 38.90844075244811,-110.63513438085685 38.67724220095734,-111.06360117772908 38.84001566645886))")

Inspect summary

out$summary

The data

out$points

Constrain search to a certain aoibbox.

An aoibbox uses the format minx, miny, maxx, maxy.

out <- bison(species="Helianthus annuus", aoibbox = '-120.31,35.81,-110.57,40.21')

Inspect summary

out$summary

The data, by default, the query only returned 10 records

head(out$points)

rbison documentation built on July 1, 2020, 10:27 p.m.