rbison vignette - wrapper to the USGS BISON API

About the package

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.

Info

See here for API docs for the BISON API.

Quick start

Install rbison

# install.packages('devtools'); library(devtools); install_github('rbison',
# 'ropensci')
library(rbison)
library(sp)
library(plyr)
library(httr)
library(rjson)
library(gridExtra)
library(mapproj)
library(ggplot2)
library(maps)
library(rgeos)
library(rgdal)

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

##   total observation fossil specimen literature unknown living centroid
## 1  4388          13    102     1267       1106    1892      8        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

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   956          32    157      718      49        1

map occurrences

bisonmap(out, tomap = "state")

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 52626       50896    105      799        118     708        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")

Constrain search with county IDs or bounding boxes

Constrain search to a certain county.

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 literature unknown centroid
## 1    24           1      3       12          1       7        1

# By default, the query only returned 10 records
head(out$points)

##                name decimalLongitude decimalLatitude occurrenceID
## 1 Helianthus annuus           -118.4           33.39   1032095838
## 2 Helianthus annuus           -118.3           34.20     45597818
## 3 Helianthus annuus           -118.0           34.00    225207520
## 4 Helianthus annuus           -118.0           34.00    225206595
## 5 Helianthus annuus           -118.0           34.00    225207727
## 6 Helianthus annuus           -118.0           34.00    225207562
##                            provider      basis
## 1              USDA PLANTS Database Literature
## 2   University of California, Davis    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 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 2 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 3 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 4 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 5 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 6 sunflower, annual 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 literature unknown centroid
## 1    24           1      3       12          1       7        1

# By default, the query only returned 10 records
head(out$points)

##                name decimalLongitude decimalLatitude occurrenceID
## 1 Helianthus annuus           -118.4           33.39   1032095838
## 2 Helianthus annuus           -118.3           34.20     45597818
## 3 Helianthus annuus           -118.0           34.00    225207520
## 4 Helianthus annuus           -118.0           34.00    225206595
## 5 Helianthus annuus           -118.0           34.00    225207727
## 6 Helianthus annuus           -118.0           34.00    225207562
##                            provider      basis
## 1              USDA PLANTS Database Literature
## 2   University of California, Davis    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 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 2 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 3 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 4 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 5 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 6 sunflower, annual 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")

Constrain search to a amorphous area.

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 literature centroid
## 1     1          1        1

# The data
head(out$points)

##                name decimalLongitude decimalLatitude occurrenceID
## 1 Helianthus annuus           -110.7           38.99   1032098012
##               provider      basis
## 1 USDA PLANTS Database Literature
##                                                     common_name geo
## 1 sunflower, annual sunflower, common sunflower, wild sunflower Yes

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

##   total observation fossil specimen literature unknown centroid
## 1   149           6      8       33         25      77        1

# The data, by default, the query only returned 10 records
head(out$points)

##                name decimalLongitude decimalLatitude occurrenceID
## 1 Helianthus annuus           -115.0           36.21    320466814
## 2 Helianthus annuus           -111.8           35.83    320466028
## 3 Helianthus annuus           -119.7           36.76     45598447
## 4 Helianthus annuus           -119.7           36.76     45598264
## 5 Helianthus annuus           -111.8           35.84   1032095762
## 6 Helianthus annuus           -115.0           36.20   1032096818
##                          provider      basis
## 1       Missouri Botanical Garden   Specimen
## 2       Missouri Botanical Garden   Specimen
## 3 University of California, Davis    Unknown
## 4 University of California, Davis    Unknown
## 5            USDA PLANTS Database Literature
## 6            USDA PLANTS Database Literature
##                                                     common_name geo
## 1 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 2 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 3 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 4 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 5 sunflower, annual sunflower, common sunflower, wild sunflower Yes
## 6 sunflower, annual sunflower, common sunflower, wild sunflower Yes