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 a node of the Global Biodiversity Information Facility (GBIF) - i.e., you can get data that's available in BISON via GBIF instead if you want.
See http://bison.usgs.ornl.gov/doc/api.jsp for API docs for the BISON API.
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.
out <- bison(species = "Helianthus annuus", count = 10)
Inspect summary
out$summary
#> total observation fossil specimen unknown living centroid
#> 1 5365 192 102 3601 1468 2 1
Map occurrences
head(out$counties)
#> record_id total county_name state
#> 1 20041 3 Dickinson County Kansas
#> 2 54103 1 Wetzel County West Virginia
#> 3 40149 1 Washita County Oklahoma
#> 4 54105 1 Wirt County West Virginia
#> 5 29025 1 Caldwell County Missouri
#> 6 40143 2 Tulsa County Oklahoma
Get data
out <- bison(species="Bison bison", count=600)
Inspect summary
out$summary
#> total observation fossil specimen unknown centroid
#> 1 1320 181 162 738 239 1
Map occurrences
bisonmap(out, tomap="state")
Get data
out <- bison(species="Aquila chrysaetos", count=600)
Inspect summary
out$summary
#> total observation fossil specimen literature unknown centroid
#> 1 91482 80582 118 785 556 9441 1
Map occurrences
bisonmap(out, tomap="points")
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")
Check out this site 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$summary
#> total observation fossil specimen unknown living centroid
#> 1 5365 192 102 3601 1468 2 1
By default, the query only returned 10 records
head(out$points)
#> name decimalLongitude decimalLatitude occurrenceID
#> 1 Helianthus annuus -72.51666 42.36666 415907013
#> 2 Helianthus annuus -103.23028 43.17889 40886844
#> 3 Helianthus annuus -102.20278 42.80472 40886841
#> 4 Helianthus annuus -112.33333 43.21667 40892620
#> 5 Helianthus annuus -99.71694 43.25963 240492543
#> 6 Helianthus annuus -103.82763 43.29724 176955413
#> provider basis
#> 1 University of Connecticut Specimen
#> 2 US National Plant Germplasm System Unknown
#> 3 US National Plant Germplasm System Unknown
#> 4 US National Plant Germplasm System Unknown
#> 5 University of Kansas Biodiversity Institute Specimen
#> 6 University of Kansas Biodiversity Institute Specimen
#> common_name geo
#> 1 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 2 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 3 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 4 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 5 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 6 annual sunflower, sunflower, common sunflower, wild sunflower Yes
Or specify county by its actual name - probably much easier.
out <- bison(species="Helianthus annuus", county = "Los Angeles")
Inspect summary
out$summary
#> total observation fossil specimen unknown centroid
#> 1 138 2 3 126 7 1
By default, the query only returned 10 records
head(out$points)
#> name decimalLongitude decimalLatitude occurrenceID
#> 1 Helianthus annuus -118.1358 34.69806 40886951
#> 2 Helianthus annuus -118.1358 34.69806 40886952
#> 3 Helianthus annuus -118.8517 34.79611 40886954
#> 4 Helianthus annuus -118.1358 34.69806 40886950
#> 5 Helianthus annuus -118.1358 34.69806 40886953
#> 6 Helianthus annuus -118.8517 34.79611 40886955
#> provider basis
#> 1 US National Plant Germplasm System Unknown
#> 2 US National Plant Germplasm System Unknown
#> 3 US National Plant Germplasm System Unknown
#> 4 US National Plant Germplasm System Unknown
#> 5 US National Plant Germplasm System Unknown
#> 6 US National Plant Germplasm System Unknown
#> common_name geo
#> 1 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 2 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 3 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 4 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 5 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 6 annual sunflower, sunflower, common sunflower, wild sunflower Yes
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")
Check out the Wikipedia page here 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$summary
#> total specimen centroid
#> 1 1 1 1
The data
out$points
#> name decimalLongitude decimalLatitude occurrenceID provider
#> 1 Helianthus annuus -110.7211 39.00903 1052407111 BISON
#> basis common_name
#> 1 Specimen annual sunflower, sunflower, common sunflower, wild sunflower
#> geo
#> 1 Yes
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$summary
#> total observation fossil specimen unknown centroid
#> 1 297 20 8 192 77 1
The data, by default, the query only returned 10 records
head(out$points)
#> name decimalLongitude decimalLatitude occurrenceID
#> 1 Helianthus annuus -120.0972 36.53167 40891669
#> 2 Helianthus annuus -120.0972 36.53167 40891613
#> 3 Helianthus annuus -119.7990 38.61761 1020768729
#> 4 Helianthus annuus -114.0000 36.83333 40892242
#> 5 Helianthus annuus -112.5256 37.04750 40892490
#> 6 Helianthus annuus -120.0972 36.53167 40886964
#> provider basis
#> 1 US National Plant Germplasm System Unknown
#> 2 US National Plant Germplasm System Unknown
#> 3 Consortium of California Herbaria Specimen
#> 4 US National Plant Germplasm System Unknown
#> 5 US National Plant Germplasm System Unknown
#> 6 US National Plant Germplasm System Unknown
#> common_name geo
#> 1 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 2 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 3 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 4 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 5 annual sunflower, sunflower, common sunflower, wild sunflower Yes
#> 6 annual sunflower, sunflower, common sunflower, wild sunflower Yes