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$summary
#> total observation fossil specimen unknown living centroid
#> 1 5108 37 102 3499 1468 2 1
Map occurrences
head(out$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$summary
#> total observation fossil specimen unknown centroid
#> 1 1432 132 164 897 239 1
Map occurrences
bisonmap(out, tomap="state")
Get data
out <- bison(species="Aquila chrysaetos", count=600)
Inspect summary
out$summary
#> total observation fossil specimen literature unknown centroid
#> 1 62862 51170 118 857 674 10043 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$summary
#> total observation fossil specimen unknown living centroid
#> 1 5108 37 102 3499 1468 2 1
By default, the query only returned 10 records
head(out$points)
#> name decimalLongitude decimalLatitude occurrenceID
#> 1 Helianthus annuus -122.6 38.11 868133992
#> 2 Helianthus annuus -120.0 34.54 866815899
#> 3 Helianthus annuus -108.6 39.06 40892504
#> 4 Helianthus annuus -117.2 34.15 867605379
#> 5 Helianthus annuus -101.2 38.48 176955508
#> 6 Helianthus annuus -118.2 35.05 40891663
#> provider basis
#> 1 Consortium of California Herbaria Specimen
#> 2 Consortium of California Herbaria Specimen
#> 3 US National Plant Germplasm System Unknown
#> 4 Consortium of California Herbaria Specimen
#> 5 University of Kansas Biodiversity Institute Specimen
#> 6 US National Plant Germplasm System Unknown
#> common_name geo
#> 1 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 2 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 3 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 4 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 5 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 6 common sunflower, wild sunflower, annual sunflower, sunflower Yes
Or specify county by its actual name - probably much easier.
out <- bison(species="Helianthus annuus", county = "Los Angeles")
Inspect summary
out$summary
#> total observation fossil specimen unknown centroid
#> 1 115 1 3 104 7 1
By default, the query only returned 10 records
head(out$points)
#> name decimalLongitude decimalLatitude occurrenceID
#> 1 Helianthus annuus -118.4 34.06 919912581
#> 2 Helianthus annuus -118.1 34.70 40886950
#> 3 Helianthus annuus -117.8 34.45 867556726
#> 4 Helianthus annuus -118.3 34.20 867698751
#> 5 Helianthus annuus -118.3 34.20 868216748
#> 6 Helianthus annuus -118.3 34.20 867920608
#> provider basis
#> 1 Consortium of California Herbaria Specimen
#> 2 US National Plant Germplasm System Unknown
#> 3 Consortium of California Herbaria Specimen
#> 4 Consortium of California Herbaria Specimen
#> 5 Consortium of California Herbaria Specimen
#> 6 Consortium of California Herbaria Specimen
#> common_name geo
#> 1 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 2 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 3 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 4 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 5 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 6 common sunflower, wild sunflower, annual sunflower, 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
#> 1 Helianthus annuus -110.7 39.01 2174803257
#> provider basis
#> 1 USDA PLANTS Database Specimen
#> common_name geo
#> 1 common sunflower, wild sunflower, annual sunflower, sunflower 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$summary
#> total observation fossil specimen unknown centroid
#> 1 241 6 8 150 77 1
The data, by default, the query only returned 10 records
head(out$points)
#> name decimalLongitude decimalLatitude occurrenceID
#> 1 Helianthus annuus -112.4 39.52 40892214
#> 2 Helianthus annuus -111.2 36.11 40892493
#> 3 Helianthus annuus -112.5 36.95 40892245
#> 4 Helianthus annuus -111.8 37.14 57033814
#> 5 Helianthus annuus -113.3 37.17 40892243
#> 6 Helianthus annuus -119.4 36.35 40892467
#> provider basis
#> 1 US National Plant Germplasm System Unknown
#> 2 US National Plant Germplasm System Unknown
#> 3 US National Plant Germplasm System Unknown
#> 4 Utah Valley State College (UVSC) Specimen
#> 5 US National Plant Germplasm System Unknown
#> 6 US National Plant Germplasm System Unknown
#> common_name geo
#> 1 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 2 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 3 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 4 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 5 common sunflower, wild sunflower, annual sunflower, sunflower Yes
#> 6 common sunflower, wild sunflower, annual sunflower, sunflower Yes