spocc
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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).
BEWARE: In cases where you request data from multiple providers, especially when including GBIF, there could be duplicate records since many providers' data eventually ends up with GBIF. See ?spocc_duplicates, after installation, for more.
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')outSummary of results - occurrences found for:
gbif : 25 records across 1 species
bison : 0 records across 1 species
inat : 0 records across 1 species
ebird : 0 records across 1 species
ecoengine : 0 records across 1 species
antweb : 0 records across 1 speciesout$gbif # just gbif dataSpecies [Accipiter striatus (25)]
First 10 rows of [Accipiter_striatus]
name longitude latitude prov key
1 Accipiter striatus -72.52547 43.13234 gbif 891035349
2 Accipiter striatus -97.19930 32.86027 gbif 891038901
3 Accipiter striatus -97.65347 30.15791 gbif 891040018
4 Accipiter striatus -71.72514 18.26982 gbif 891035119
5 Accipiter striatus -122.43980 37.48967 gbif 891040169
6 Accipiter striatus -76.64497 41.85597 gbif 891043765
7 Accipiter striatus -73.06720 43.63152 gbif 891048899
8 Accipiter striatus -99.09873 26.49104 gbif 891049443
9 Accipiter striatus -117.14734 32.70358 gbif 891056214
10 Accipiter striatus -97.88279 26.10227 gbif 891050439
.. ... ... ... ... ...Get fine-grained detail over each data source by passing on parameters to the packge rebird in this example.
out <- occ(query='Setophaga caerulescens', from='ebird', ebirdopts=list(region='US'))
out$ebird # just ebird dataSpecies [Setophaga caerulescens (25)]
First 10 rows of [Setophaga_caerulescens]
name longitude latitude prov comName howMany locID
1 Setophaga caerulescens -82.27411 35.71525 ebird Black-throated Blue Warbler 3 L808055
2 Setophaga caerulescens -81.68619 36.16935 ebird Black-throated Blue Warbler 1 L2377362
3 Setophaga caerulescens -73.05840 44.76782 ebird Black-throated Blue Warbler 1 L1042249
4 Setophaga caerulescens -83.91559 35.23377 ebird Black-throated Blue Warbler 3 L1117355
5 Setophaga caerulescens -71.33629 44.07229 ebird Black-throated Blue Warbler 1 L3019553
6 Setophaga caerulescens -69.88103 44.53983 ebird Black-throated Blue Warbler 1 L668744
7 Setophaga caerulescens -83.03123 35.15585 ebird Black-throated Blue Warbler 4 L3018347
8 Setophaga caerulescens -72.36832 44.42826 ebird Black-throated Blue Warbler 1 L3016946
9 Setophaga caerulescens -76.28847 42.43226 ebird Black-throated Blue Warbler 1 L453322
10 Setophaga caerulescens -72.19843 42.93351 ebird Black-throated Blue Warbler 2 L160223
.. ... ... ... ... ... ... ...
Variables not shown: locName (chr), locationPrivate (lgl), obsDt (chr), obsReviewed (lgl), obsValid
(lgl)
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')
