rvertnet is a client for interacting with VertNet.org.
You can install the stable version from CRAN:
install.packages("rvertnet")
Or the development version from GitHub using the devtools package:
install.packages("devtools")
devtools::install_github("ropensci/rvertnet")
library('rvertnet')
Search for Aves in the state of California, limit to 10 records
res <- searchbyterm(class = "Aves", state = "California", limit = 10, verbose = FALSE)
All major functions (searchbyterm(), spatialsearch(), vertsearch()) give back a meta (for metadata, in a list) and data (for data, in a data.frame) slot. The metadata:
res$meta
#> $request_date
#> [1] "2017-08-14T22:00:59.132690"
#>
#> $response_records
#> [1] 10
#>
#> $submitted_query
#> [1] "class:Aves stateprovince:California"
#>
#> $request_origin
#> [1] "45.523452,-122.676207"
#>
#> $limit
#> [1] 10
#>
#> $last_cursor
#> [1] "False:Cu8GCsoECpwE9wAAABn_____jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wAA_3RtoKCZi4ygoP8AAP9dno-PmpGYlpGa_wAA_3N0bZaRm5qH_wAA_12biJz_AAD_c3Rtm5CcoJab_wAA_12cipKJ0J2WjZvSjI-anJaSmpGM0JeLi4_Sno2ci5CM0puei56dnoya0pKKjJqKktKYipab0pyKkonSnZaNm9LLy87JydKMmpab0s3Mz8zMxsj_AAD_c3-cipKJ0J2WjZvSjI-anJaSmpGM0JeLi4_Sno2ci5CM0puei56dnoya0pKKjJqKktKYipab0pyKkonSnZaNm9LLy87JydKMmpab0s3Mz8zMxsj_AAD__wD-__6MgYmajYuRmovSj5CNi56T3paRm5qH0s3PzszSz8fSz8f_AHRtoKCZi4ygoP8AXZ6Pj5qRmJaRmv8Ac3RtlpGbmof_AF2biJz_AHN0bZuQnKCWm_8AXZyKkonQnZaNm9KMj5qclpKakYzQl4uLj9KejZyLkIzSm56Lnp2ejJrSkoqMmoqS0piKlpvSnIqSidKdlo2b0svLzsnJ0oyalpvSzczPzMzGyP8Ac3-cipKJ0J2WjZvSjI-anJaSmpGM0JeLi4_Sno2ci5CM0puei56dnoya0pKKjJqKktKYipab0pyKkonSnZaNm9LLy87JydKMmpab0s3Mz8zMxsj_AP_-EAohBN0EkB08Gxk5AAAAAOb___9IClAAWgsJ4h5N-19FzJ8QAmDRs6XyARINRG9jdW1lbnRJbmRleBruAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKE9SIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKElTICJyYXRvbV9jbGFzcyIgImF2ZXMiKSkgKFFUICJDYWxpZm9ybmlhIiAicnRleHRfc3RhdGVwcm92aW5jZSIpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#>
#> $query_version
#> [1] "search.py 2016-08-15T16:43+02:00"
#>
#> $matching_records
#> [1] ">10000"
#>
#> $api_version
#> [1] "api.py 2017-01-12T20:08-03:00"
The data
res$data
#> # A tibble: 10 x 70
#> modified language license
#> <chr> <chr> <chr>
#> 1 2015-01-06 en CCBY
#> 2 2015-01-06 en CCBY
#> 3 2015-01-06 en CCBY
#> 4 2015-08-26 13:10:07.0 en CC0
#> 5 2015-08-26 13:10:07.0 en CC0
#> 6 2015-08-26 13:10:07.0 en CC0
#> 7 2015-08-26 13:10:07.0 en CC0
#> 8 2016-05-18 09:27:29.0 en CC0
#> 9 2016-05-18 09:27:29.0 en CC0
#> 10 2016-05-18 09:27:29.0 en CC0
#> # ... with 67 more variables: accessrights <chr>,
#> # bibliographiccitation <chr>, references <chr>, institutionid <chr>,
#> # institutioncode <chr>, collectioncode <chr>, basisofrecord <chr>,
#> # dynamicproperties <chr>, occurrenceid <chr>, catalognumber <chr>,
#> # recordedby <chr>, individualcount <chr>, sex <chr>,
#> # occurrencestatus <chr>, preparations <chr>, associatedmedia <chr>,
#> # othercatalognumbers <chr>, occurrenceremarks <chr>, organismid <chr>,
#> # previousidentifications <chr>, eventdate <chr>, startdayofyear <chr>,
#> # enddayofyear <chr>, year <chr>, month <chr>, day <chr>,
#> # verbatimeventdate <chr>, samplingprotocol <chr>,
#> # highergeography <chr>, continent <chr>, country <chr>,
#> # countrycode <chr>, stateprovince <chr>, county <chr>, locality <chr>,
#> # verbatimlocality <chr>, locationaccordingto <chr>,
#> # locationremarks <chr>, decimallatitude <chr>, decimallongitude <chr>,
#> # geodeticdatum <chr>, coordinateuncertaintyinmeters <chr>,
#> # coordinateprecision <chr>, verbatimcoordinates <chr>,
#> # verbatimcoordinatesystem <chr>, georeferencedby <chr>,
#> # georeferenceddate <chr>, georeferenceprotocol <chr>,
#> # georeferencesources <chr>, georeferenceverificationstatus <chr>,
#> # identificationqualifier <chr>, identifiedby <chr>,
#> # dateidentified <chr>, identificationverificationstatus <chr>,
#> # scientificname <chr>, higherclassification <chr>, kingdom <chr>,
#> # phylum <chr>, class <chr>, order <chr>, family <chr>, genus <chr>,
#> # specificepithet <chr>, infraspecificepithet <chr>, taxonrank <chr>,
#> # vernacularname <chr>, nomenclaturalcode <chr>
Search for Mustela nigripes in the states of Wyoming or South Dakota, limit to 20 records
res <- searchbyterm(specificepithet = "nigripes", genus = "Mustela", state = "(wyoming OR south dakota)", limit = 20, verbose = FALSE)
res$data
#> # A tibble: 19 x 73
#> modified language license
#> <chr> <chr> <chr>
#> 1 2010-01-14 13:06:23.0 en CC-BY
#> 2 2011-11-17 12:02:57.0 en CC0
#> 3 2013-08-07 en <NA>
#> 4 2015-11-23 09:17:09.0 en CC0
#> 5 2016-02-01 17:40:23.0 en CC0
#> 6 2016-04-12 00:24:00.0 en CC0
#> 7 2016-11-15 en CC0
#> 8 <NA> <NA> CC0
#> 9 <NA> <NA> CC0
#> 10 <NA> <NA> CC0
#> 11 <NA> <NA> CC0
#> 12 <NA> <NA> CC0
#> 13 <NA> <NA> CC0
#> 14 <NA> <NA> CC0
#> 15 <NA> <NA> CC0
#> 16 <NA> <NA> CC0
#> 17 <NA> <NA> CC0
#> 18 <NA> <NA> CC0
#> 19 <NA> <NA> CC0
#> # ... with 70 more variables: accessrights <chr>,
#> # bibliographiccitation <chr>, references <chr>, institutionid <chr>,
#> # institutioncode <chr>, collectioncode <chr>, datasetname <chr>,
#> # basisofrecord <chr>, dynamicproperties <chr>, occurrenceid <chr>,
#> # catalognumber <chr>, recordnumber <chr>, recordedby <chr>,
#> # individualcount <chr>, sex <chr>, occurrencestatus <chr>,
#> # preparations <chr>, othercatalognumbers <chr>,
#> # occurrenceremarks <chr>, organismid <chr>,
#> # previousidentifications <chr>, eventdate <chr>, eventtime <chr>,
#> # startdayofyear <chr>, enddayofyear <chr>, year <chr>, month <chr>,
#> # day <chr>, verbatimeventdate <chr>, samplingprotocol <chr>,
#> # eventremarks <chr>, highergeography <chr>, continent <chr>,
#> # country <chr>, countrycode <chr>, stateprovince <chr>, county <chr>,
#> # locality <chr>, verbatimlocality <chr>,
#> # minimumelevationinmeters <chr>, maximumelevationinmeters <chr>,
#> # locationaccordingto <chr>, locationremarks <chr>,
#> # decimallatitude <chr>, decimallongitude <chr>, geodeticdatum <chr>,
#> # coordinateuncertaintyinmeters <chr>, verbatimcoordinates <chr>,
#> # verbatimcoordinatesystem <chr>, georeferencedby <chr>,
#> # georeferenceddate <chr>, georeferenceprotocol <chr>,
#> # georeferencesources <chr>, georeferenceverificationstatus <chr>,
#> # identificationqualifier <chr>, identifiedby <chr>,
#> # dateidentified <chr>, identificationverificationstatus <chr>,
#> # scientificname <chr>, higherclassification <chr>, kingdom <chr>,
#> # phylum <chr>, class <chr>, order <chr>, family <chr>, genus <chr>,
#> # specificepithet <chr>, taxonrank <chr>, vernacularname <chr>,
#> # nomenclaturalcode <chr>
Search for class Aves, in the state of Nevada, with a coordinate uncertainty range (in meters) of less than 25 meters
res <- searchbyterm(class = "Aves", stateprovince = "Nevada", error = "<25", verbose = FALSE)
res$data
#> # A tibble: 8 x 70
#> modified language license
#> <chr> <chr> <chr>
#> 1 2013-01-05 17:46:29.0 en CC0
#> 2 2015-06-22 12:58:04.0 en CC0
#> 3 2016-05-18 11:06:12.0 en <NA>
#> 4 2016-05-18 11:06:12.0 en <NA>
#> 5 2016-05-18 11:06:12.0 en <NA>
#> 6 2016-05-18 11:06:12.0 en <NA>
#> 7 2016-05-18 11:06:12.0 en <NA>
#> 8 2016-05-18 11:06:12.0 en <NA>
#> # ... with 67 more variables: accessrights <chr>,
#> # bibliographiccitation <chr>, references <chr>, institutionid <chr>,
#> # collectionid <chr>, institutioncode <chr>, collectioncode <chr>,
#> # basisofrecord <chr>, dynamicproperties <chr>, occurrenceid <chr>,
#> # catalognumber <chr>, recordnumber <chr>, recordedby <chr>,
#> # individualcount <chr>, sex <chr>, lifestage <chr>, preparations <chr>,
#> # associatedmedia <chr>, othercatalognumbers <chr>,
#> # occurrenceremarks <chr>, organismid <chr>,
#> # previousidentifications <chr>, eventdate <chr>, startdayofyear <chr>,
#> # enddayofyear <chr>, year <chr>, month <chr>, day <chr>,
#> # verbatimeventdate <chr>, habitat <chr>, samplingprotocol <chr>,
#> # highergeography <chr>, continent <chr>, country <chr>,
#> # stateprovince <chr>, county <chr>, locality <chr>,
#> # verbatimlocality <chr>, minimumelevationinmeters <chr>,
#> # maximumelevationinmeters <chr>, locationaccordingto <chr>,
#> # decimallatitude <chr>, decimallongitude <chr>, geodeticdatum <chr>,
#> # coordinateuncertaintyinmeters <chr>, verbatimcoordinates <chr>,
#> # verbatimcoordinatesystem <chr>, georeferencedby <chr>,
#> # georeferenceddate <chr>, georeferenceprotocol <chr>,
#> # georeferencesources <chr>, georeferenceverificationstatus <chr>,
#> # identificationqualifier <chr>, identifiedby <chr>,
#> # dateidentified <chr>, identificationverificationstatus <chr>,
#> # scientificname <chr>, higherclassification <chr>, kingdom <chr>,
#> # phylum <chr>, class <chr>, order <chr>, family <chr>, genus <chr>,
#> # specificepithet <chr>, infraspecificepithet <chr>,
#> # nomenclaturalcode <chr>
Spatial search service allows only to search on a point defined by latitude and longitude pair, with a radius (meters) from that point. All three parameters are required.
res <- spatialsearch(lat = 33.529, lon = -105.694, radius = 2000, limit = 10, verbose = FALSE)
res$data
#> # A tibble: 10 x 60
#> modified language accessrights
#> <chr> <chr> <chr>
#> 1 2014-09-09 14:04:14.0 en http://vertnet.org/resources/norms.html
#> 2 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 3 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 4 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 5 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 6 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 7 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 8 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 9 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> 10 2015-08-03 19:48:08.0 en http://vertnet.org/resources/norms.html
#> # ... with 57 more variables: bibliographiccitation <chr>,
#> # references <chr>, institutionid <chr>, institutioncode <chr>,
#> # collectioncode <chr>, basisofrecord <chr>, dynamicproperties <chr>,
#> # occurrenceid <chr>, catalognumber <chr>, recordnumber <chr>,
#> # recordedby <chr>, individualcount <chr>, sex <chr>,
#> # preparations <chr>, othercatalognumbers <chr>,
#> # occurrenceremarks <chr>, organismid <chr>,
#> # previousidentifications <chr>, eventdate <chr>, startdayofyear <chr>,
#> # enddayofyear <chr>, year <chr>, month <chr>, day <chr>,
#> # verbatimeventdate <chr>, highergeography <chr>, continent <chr>,
#> # country <chr>, stateprovince <chr>, county <chr>, locality <chr>,
#> # verbatimlocality <chr>, minimumelevationinmeters <chr>,
#> # maximumelevationinmeters <chr>, locationaccordingto <chr>,
#> # decimallatitude <chr>, decimallongitude <chr>, geodeticdatum <chr>,
#> # coordinateuncertaintyinmeters <chr>, georeferencedby <chr>,
#> # georeferenceddate <chr>, georeferenceprotocol <chr>,
#> # georeferencesources <chr>, georeferenceverificationstatus <chr>,
#> # identificationqualifier <chr>, identifiedby <chr>,
#> # identificationverificationstatus <chr>, scientificname <chr>,
#> # higherclassification <chr>, kingdom <chr>, phylum <chr>, class <chr>,
#> # order <chr>, family <chr>, genus <chr>, specificepithet <chr>,
#> # nomenclaturalcode <chr>
vertsearch() provides a simple full text search against all fields. For more info see the docs. An example:
res <- vertsearch(taxon = "aves", state = "california", limit = 10)
res$data
#> # A tibble: 10 x 60
#> modified language license accessrights
#> <chr> <chr> <chr> <chr>
#> 1 2015-01-06 en CCBY <NA>
#> 2 2015-01-06 en CCBY <NA>
#> 3 2015-01-06 en CCBY <NA>
#> 4 2015-10-13 en CC0 http://vertnet.org/resources/norms.html
#> 5 2015-10-13 en CC0 http://vertnet.org/resources/norms.html
#> 6 2016-08-25 en CC0 http://vertnet.org/resources/norms.html
#> 7 2016-08-25 en CC0 http://vertnet.org/resources/norms.html
#> 8 2016-08-25 en CC0 http://vertnet.org/resources/norms.html
#> 9 2016-08-25 en CC0 http://vertnet.org/resources/norms.html
#> 10 2016-08-25 en CC0 http://vertnet.org/resources/norms.html
#> # ... with 56 more variables: bibliographiccitation <chr>,
#> # references <chr>, institutionid <chr>, institutioncode <chr>,
#> # collectioncode <chr>, basisofrecord <chr>, dynamicproperties <chr>,
#> # occurrenceid <chr>, catalognumber <chr>, recordedby <chr>, sex <chr>,
#> # lifestage <chr>, occurrencestatus <chr>, preparations <chr>,
#> # othercatalognumbers <chr>, occurrenceremarks <chr>, eventdate <chr>,
#> # startdayofyear <chr>, enddayofyear <chr>, year <chr>, month <chr>,
#> # day <chr>, verbatimeventdate <chr>, highergeography <chr>,
#> # continent <chr>, country <chr>, countrycode <chr>,
#> # stateprovince <chr>, county <chr>, locality <chr>,
#> # verbatimlocality <chr>, locationremarks <chr>, decimallatitude <chr>,
#> # decimallongitude <chr>, geodeticdatum <chr>,
#> # coordinateuncertaintyinmeters <chr>, coordinateprecision <chr>,
#> # georeferencedby <chr>, georeferenceddate <chr>,
#> # georeferenceprotocol <chr>, georeferencesources <chr>,
#> # georeferenceverificationstatus <chr>, georeferenceremarks <chr>,
#> # scientificname <chr>, higherclassification <chr>, kingdom <chr>,
#> # phylum <chr>, class <chr>, order <chr>, family <chr>, genus <chr>,
#> # specificepithet <chr>, infraspecificepithet <chr>, taxonrank <chr>,
#> # vernacularname <chr>, nomenclaturalcode <chr>
Limit the number of records returned (under 1000)
res <- vertsearch("(kansas state OR KSU)", limit = 200)
res$data
#> # A tibble: 200 x 78
#> modified language license
#> <chr> <chr> <chr>
#> 1 2013-02-20 16:33:54.0 en CC0
#> 2 2014-10-29 11:49:14.0 en CC-BY
#> 3 2014-10-29 11:49:17.0 en CC-BY
#> 4 2014-10-29 11:52:29.0 en CC-BY
#> 5 2014-10-29 11:55:30.0 en CC-BY
#> 6 2014-10-29 11:55:31.0 en CC-BY
#> 7 2014-10-29 11:59:35.0 en CC-BY
#> 8 2014-10-29 12:00:01.0 en CC-BY
#> 9 2014-10-29 12:00:23.0 en CC-BY
#> 10 2014-10-29 12:02:11.0 en CC-BY
#> # ... with 190 more rows, and 75 more variables: accessrights <chr>,
#> # bibliographiccitation <chr>, references <chr>, institutionid <chr>,
#> # collectionid <chr>, institutioncode <chr>, collectioncode <chr>,
#> # datasetname <chr>, basisofrecord <chr>, dynamicproperties <chr>,
#> # occurrenceid <chr>, catalognumber <chr>, recordnumber <chr>,
#> # recordedby <chr>, individualcount <chr>, sex <chr>, lifestage <chr>,
#> # establishmentmeans <chr>, occurrencestatus <chr>, preparations <chr>,
#> # disposition <chr>, othercatalognumbers <chr>, occurrenceremarks <chr>,
#> # organismid <chr>, previousidentifications <chr>, fieldnumber <chr>,
#> # eventdate <chr>, startdayofyear <chr>, enddayofyear <chr>, year <chr>,
#> # month <chr>, day <chr>, verbatimeventdate <chr>,
#> # samplingprotocol <chr>, highergeography <chr>, continent <chr>,
#> # country <chr>, countrycode <chr>, stateprovince <chr>, county <chr>,
#> # locality <chr>, verbatimlocality <chr>,
#> # minimumelevationinmeters <chr>, maximumelevationinmeters <chr>,
#> # locationaccordingto <chr>, decimallatitude <chr>,
#> # decimallongitude <chr>, geodeticdatum <chr>,
#> # coordinateuncertaintyinmeters <chr>, verbatimcoordinates <chr>,
#> # verbatimcoordinatesystem <chr>, footprintwkt <chr>,
#> # georeferencedby <chr>, georeferenceddate <chr>,
#> # georeferenceprotocol <chr>, georeferencesources <chr>,
#> # georeferenceverificationstatus <chr>, georeferenceremarks <chr>,
#> # identificationqualifier <chr>, identifiedby <chr>,
#> # dateidentified <chr>, identificationverificationstatus <chr>,
#> # identificationremarks <chr>, scientificname <chr>,
#> # higherclassification <chr>, kingdom <chr>, phylum <chr>, class <chr>,
#> # order <chr>, family <chr>, genus <chr>, specificepithet <chr>,
#> # infraspecificepithet <chr>, taxonrank <chr>, nomenclaturalcode <chr>
Pass output of vertsearch() to a map
out <- vertsearch(tax = "(mustela nivalis OR mustela erminea)")
vertmap(out)
For searchbyterm(), spatialsearch(), and vertsearch(), you can request more than 1000 records. VertNet limits each request to 1000 records, but internally in this package, if you request more than 1000 records, we'll continue to send requests to get all the records you want. See the VertNet docs for more information on this.
bigsearch() specifies a termwise search (like searchbyterm()), but requests that all available records be made available for download as a tab-delimited text file.
bigsearch(genus = "ochotona", rfile = "mydata", email = "you@gmail.com")
#> Processing request...
#>
#> Download of records file 'mydata' requested for 'you@gmail.com'
#>
#> Query/URL: "http://api.vertnet-portal.appspot.com/api/download?q=%7B%22q%22:%22genus:ochotona%22,%22n%22:%22mydata%22,%22e%22:%22you@gmail.com%22%7D"
#>
#> Thank you! Download instructions will be sent by email.
In the previous examples, we've suppressed messages for more concise output, but you can set verbose=TRUE to get helpful messages - verbose=TRUE is also the default setting so if you don't specify that parameter messages will be printed to the console.
res <- searchbyterm(class = "Aves", state = "California", limit = 10, verbose = TRUE)