natserv
'NatureServe' Interface
Interface to 'NatureServe' (< http://www.natureserve.org>). Includes methods to get data, image metadata, search taxonomic names, and make maps.
natserv NatureServe R client
NatureServe is a non-profit organization that provides wildlife conservation related data to various groups including the public.
All functions in this package are prefixed with ns_ to prevent
collision with other pkgs.
Three NatureServe web services are available in this package:
- Name lookup (
ns_search) lookup species Unique IDs (UID) by name. These UIDs are required for access to the more detailed services. - Image lookup (
ns_images) search for metadata for NatureServe images, including the URL's for the image files themselves. - Fetch data (
ns_data) on over 70,000 of the plant and animal species of the United States and Canada.
You'll need an API key to use this package. Get one by signing up at https://services.natureserve.org/developer/index.jsp
See also the taxize book for a manual on working with taxonomic data in R, including with NatureServe data.
Stable version from CRAN
install.packages("natserv")Development version
remotes::install_github("ropensci/natserv")library('natserv')search
ns_search(x = "Helianthus annuus")#> # A tibble: 1 x 4#> globalSpeciesUid jurisdictionScien… commonName natureServeExplorerURI #> <chr> <chr> <chr> <chr> #> 1 ELEMENT_GLOBAL.2.… Helianthus annuus Common Su… http://explorer.natures…data
res <- ns_data(uid = 'ELEMENT_GLOBAL.2.100925')names(res$ELEMENT_GLOBAL.2.100925)#> [1] "uid" "speciesCode" #> [3] "natureserve_uri" "classification" #> [5] "economicAttributes" "ecologyAndLifeHistory"#> [7] "license" "references" #> [9] "conservationStatus" "managementSummary" #> [11] "distribution"dig into distribution in various watersheds
res$ELEMENT_GLOBAL.2.100925$distribution$watersheds#> # A tibble: 527 x 4#> type watershedName watershedCode speciesOccurrenceCount#> <chr> <chr> <chr> <chr> #> 1 HUC-8 Housatonic 01100005 1 #> 2 HUC-8 Upper Hudson 02020001 3 #> 3 HUC-8 Middle Hudson 02020006 1 #> 4 HUC-8 Hudson-Wappinger 02020008 2 #> 5 HUC-8 Noxubee 03160108 1 #> 6 HUC-8 Lower Leaf 03170005 1 #> 7 HUC-8 Pascagoula 03170006 2 #> 8 HUC-8 Black 03170007 1 #> 9 HUC-8 Escatawpa 03170008 1 #> 10 HUC-8 Black 04150101 1 #> # … with 517 more rowsimage metadata
res <- ns_images(commonName = "*eagle", resolution = 'thumbnail')res$images[[1]][1:5]#> $id#> [1] "15512"#> #> $scientificName#> [1] "Haliaeetus leucocephalus"#> #> $commonName#> [1] "Bald Eagle"#> #> $otherCommonName#> [1] "bald eagle"#> #> $otherCommonName#> [1] "pygargue à tête blanche"Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
natservin R doingcitation(package = 'natserv') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
News
natserv 0.3.0
NEW FEATURES
- gains a vignette: "Introduction to
natserve- An R package to wrap NatureServe's database API from rOpenSci" (#6) (#16) all work done by @mairindeith - thanks!
MINOR IMPROVEMENTS
- add
vcrfor tests so that http requests are cached (#18) - link to taxize book in readme and vignette (#15)
- improve failure behavior. the NatureServe API returns 200 on no result found, so we have to do gymnastics to catch that scenario (#9)
BUG FIXES
- bug in
ns_data()fixed related to subnations (#10) - a bunch of checks added within
ns_data(),ns_images(), andns_search()to catch common bad inputs to the functions (#11) - fixed bug in internal function
check_uid()that was throwing warnings inns_data()when passing more than one input (#14)
natserv 0.1.4
MINOR IMPROVEMENTS
natservnow requirescrul>= 0.2.0, which fixed URL encoding to make our work innatserveasier.
natserv 0.1.0
NEW FEATURES
- released to CRAN