spocc
spocc = SPecies OCCurrence data
At rOpenSci, we have been writing R packages to interact with many sources of species occurrence data, including GBIF, Vertnet, BISON, iNaturalist, the Berkeley ecoengine, and AntWeb. spocc is an R package to query and collect species occurrence data from many sources. The goal is to wrap functions in other R packages to make a seamless experience across data sources for the user.
The inspiration for this comes from users requesting a more seamless experience across data sources, and from our work on a similar package for taxonomy data (taxize).
Contributing
See CONTRIBUTING.md
Quick start
Install
Install spocc
install.packages("spocc", dependencies = TRUE)Or the development version
install.packages("devtools")
library(devtools)
install_github("ropensci/spocc")
library(spocc)Get data
Get data from GBIF
out <- occ(query='Accipiter striatus', from='gbif')
out$gbif # just gbif data$gbif
$gbif$meta
$gbif$meta$source
[1] "gbif"
$gbif$meta$time
[1] "2013-12-11 10:02:45 PST"
$gbif$meta$query
[1] "Accipiter striatus"
$gbif$meta$type
[1] "sci"
$gbif$meta$opts
list()
$gbif$data
$gbif$data$Accipiter_striatus
name key longitude latitude prov
1 Accipiter striatus Vieillot, 1808 773408845 -97.27682 32.87642 gbif
2 Accipiter striatus Vieillot, 1808 768992325 -76.10433 4.72375 gbif
3 Accipiter striatus Vieillot, 1808 773414146 -122.26848 37.77092 gbif
4 Accipiter striatus Vieillot, 1808 773440541 -98.00115 32.80013 gbif
5 Accipiter striatus Vieillot, 1808 773423188 -76.54262 38.68847 gbif
6 Accipiter striatus Vieillot, 1808 773432602 -122.78289 38.61318 gbif
7 Accipiter striatus Vieillot, 1808 773430206 -117.06342 32.55171 gbif
8 Accipiter striatus Vieillot, 1808 833024105 -105.15587 40.67825 gbif
9 Accipiter striatus Vieillot, 1808 NA NA NA gbif
10 Accipiter striatus Vieillot, 1808 579130954 -74.44419 40.54073 gbif
11 Accipiter striatus Vieillot, 1808 579131911 -76.69865 39.88886 gbif
12 Accipiter striatus Vieillot, 1808 579132307 -75.55195 39.60463 gbif
13 Accipiter striatus Vieillot, 1808 579134716 -96.97675 32.64104 gbif
14 Accipiter striatus Vieillot, 1808 579138808 -73.57194 41.00291 gbif
15 Accipiter striatus Vieillot, 1808 579149929 -123.96475 49.23553 gbif
16 Accipiter striatus Vieillot, 1808 579157816 -70.40314 41.68471 gbif
17 Accipiter striatus Vieillot, 1808 579125251 -84.13030 33.97565 gbif
18 Accipiter striatus Vieillot, 1808 579127561 -90.07058 30.01456 gbif
19 Accipiter striatus Vieillot, 1808 579128452 -105.20556 39.66553 gbif
20 Accipiter striatus Vieillot, 1808 818461023 -111.73395 33.36145 gbif
....(remainder of output cut off)
Get fine-grained detail over each data source by passing on parameters to the packge rebird in this example.
out <- occ(query='Setophaga caerulescens', from='ebird', ebirdopts=list(region='US'))
out$ebird # just ebird data$meta
$meta$source
[1] "ebird"
$meta$time
[1] "2013-12-11 10:04:37 PST"
$meta$query
[1] "Setophaga caerulescens"
$meta$type
[1] "sci"
$meta$opts
$meta$opts$region
[1] "US"
$data
$data$Setophaga_caerulescens
comName howMany lat lng locID locName
1 Black-throated Blue Warbler 1 40.93444 -73.84513 L2374154 NY - Sarah Lawrence College
2 Black-throated Blue Warbler 1 25.73408 -80.31086 L200830 A. D. Barnes Park
3 Black-throated Blue Warbler 1 26.17131 -80.16149 L710596 John D. Easterlin County Park
4 Black-throated Blue Warbler 1 26.23507 -80.19144 L818386 Coconut Creek-Pompano CBC area
5 Black-throated Blue Warbler 1 25.91066 -80.33196 L1875938 Miami Lakes West Park
6 Black-throated Blue Warbler 1 25.32295 -80.83315 L123123 Everglades NP--Mahogany Hammock
7 Black-throated Blue Warbler 1 36.19909 -105.88400 L1824677 Dixon/El Bosque
8 Black-throated Blue Warbler 1 25.67330 -80.15820 L127423 Bill Baggs Cape Florida SP
9 Black-throated Blue Warbler 1 28.79362 -82.52210 L2440885 Home
10 Black-throated Blue Warbler 1 25.73918 -80.30943 L1663905 Miami - AD Barnes Park - Nature Center
locationPrivate obsDt obsReviewed obsValid name prov
1 TRUE 2013-12-06 13:00 TRUE TRUE Setophaga caerulescens ebird
2 FALSE 2013-12-06 12:04 FALSE TRUE Setophaga caerulescens ebird
3 FALSE 2013-12-06 09:10 FALSE TRUE Setophaga caerulescens ebird
4 TRUE 2013-12-05 08:45 FALSE TRUE Setophaga caerulescens ebird
5 TRUE 2013-12-03 09:15 FALSE TRUE Setophaga caerulescens ebird
6 FALSE 2013-12-01 11:20 FALSE TRUE Setophaga caerulescens ebird
7 TRUE 2013-12-01 08:40 TRUE TRUE Setophaga caerulescens ebird
8 FALSE 2013-12-01 06:50 FALSE TRUE Setophaga caerulescens ebird
9 TRUE 2013-11-30 16:05 TRUE TRUE Setophaga caerulescens ebird
10 TRUE 2013-11-28 FALSE TRUE Setophaga caerulescens ebird
Get data from many sources in a single call
ebirdopts = list(region='US'); gbifopts = list(country='US')
out <- occ(query='Setophaga caerulescens', from=c('gbif','bison','inat','ebird'), gbifopts=gbifopts, ebirdopts=ebirdopts)
head(occ2df(out)); tail(occ2df(out)) name longitude latitude prov
1 Setophaga caerulescens -122.32551 37.26128 gbif
2 Setophaga caerulescens -117.04148 32.79913 gbif
3 Setophaga caerulescens -87.61893 41.87652 gbif
4 Setophaga caerulescens -80.79602 25.39812 gbif
5 Setophaga caerulescens -80.31086 25.73408 gbif
6 Setophaga caerulescens -69.99167 41.91779 gbif
name longitude latitude prov
91 Setophaga caerulescens 25.91066 -80.33196 ebird
92 Setophaga caerulescens 25.32295 -80.83315 ebird
93 Setophaga caerulescens 36.19909 -105.88400 ebird
94 Setophaga caerulescens 25.67330 -80.15820 ebird
95 Setophaga caerulescens 28.79362 -82.52210 ebird
96 Setophaga caerulescens 25.73918 -80.30943 ebird
Make maps
Leaflet
spp <- c('Danaus plexippus','Accipiter striatus','Pinus contorta')
dat <- occ(query = spp, from = 'gbif', gbifopts = list(hasCoordinate=TRUE))
data <- occ2df(dat)
mapleaflet(data = data, dest = ".")
Github gist
spp <- c('Danaus plexippus','Accipiter striatus','Pinus contorta')
dat <- occ(query=spp, from='gbif', gbifopts=list(hasCoordinate=TRUE))
dat <- fixnames(dat)
dat <- occ2df(dat)
mapgist(data=dat, color=c("#976AAE","#6B944D","#BD5945"))
ggplot2
ecoengine_data <- occ(query = 'Lynx rufus californicus', from = 'ecoengine')
mapggplot(ecoengine_data)
Base R plots
spnames <- c('Accipiter striatus', 'Setophaga caerulescens', 'Spinus tristis')
out <- occ(query=spnames, from='gbif', gbifopts=list(hasCoordinate=TRUE))
plot(out, cex=1, pch=10)
Please report any issues or bugs](https://github.com/ropensci/spocc/issues).
License: MIT
This package is part of the rOpenSci project.
To cite package spocc in publications use:
To cite package ‘spocc’ in publications use:
Scott Chamberlain, Karthik Ram and Ted Hart (2014). spocc: R interface to many species occurrence data sources. R package version 0.1.0.
https://github.com/ropensci/spocc
A BibTeX entry for LaTeX users is
@Manual{,
title = {spocc: R interface to many species occurrence data sources},
author = {Scott Chamberlain and Karthik Ram and Ted Hart},
year = {2014},
note = {R package version 0.1.0},
url = {https://github.com/ropensci/spocc},
}Get citation information for spocc in R doing citation(package = 'spocc')
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