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, messages = 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] "2018-04-17T06:14:32.384580"
#>
#> $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:Cq8FCooDCtwC9wAAABn_____jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wAA_3RtoKCZi4ygoP8AAP9dno-PmpGYlpGa_wAA_3N0bZaRm5qH_wAA_12biJz_AAD_c3Rtm5CcoJab_wAA_12cnozQkI2R0IqNkdKcnouek5CY0pyejNKQjZHSzs_Pzs7_AAD_c3-cnozQkI2R0IqNkdKcnouek5CY0pyejNKQjZHSzs_Pzs7_AAD__wD-__6MgYmajYuRmovSj5CNi56T3paRm5qH0s3PzszSz8fSz8f_AHRtoKCZi4ygoP8AXZ6Pj5qRmJaRmv8Ac3RtlpGbmof_AF2biJz_AHN0bZuQnKCWm_8AXZyejNCQjZHQio2R0pyei56TkJjSnJ6M0pCNkdLOz8_Ozv8Ac3-cnozQkI2R0IqNkdKcnouek5CY0pyejNKQjZHSzs_Pzs7_AP_-EAohBN0EkB08Gxk5AAAAAOb___9IClAAWgsJdSRwg5uy6lIQAmDd8uOABxINRG9jdW1lbnRJbmRleBruAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKE9SIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKElTICJyYXRvbV9jbGFzcyIgImF2ZXMiKSkgKFFUICJDYWxpZm9ybmlhIiAicnRleHRfc3RhdGVwcm92aW5jZSIpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#>
#> $query_version
#> [1] "search.py 2016-08-15T16:43+02:00"
#>
#> $matching_records
#> [1] ">10000"
#>
#> $api_version
#> [1] "api.py 2017-11-24T12:16-03:00"
The data
res$data
#> # A tibble: 10 x 57
#> higherclassification stateprovince basisofrecord month decimallongitude
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Animalia | Chordata… California PreservedSpe… 2 -121.7833
#> 2 Animalia | Chordata… California PreservedSpe… 6 -122.15
#> 3 Animalia | Chordata… California PreservedSpe… 5 -120.9014
#> 4 Animalia; Chordata;… California PreservedSpe… 1 -121.93300
#> 5 Animalia; Chordata;… California PreservedSpe… 1 -121.93300
#> 6 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> 7 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> 8 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> 9 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> 10 Animalia; Chordata;… California PreservedSpe… 6 -121.85760
#> # ... with 52 more variables: phylum <chr>, references <chr>, year <chr>,
#> # startdayofyear <chr>, taxonrank <chr>, specificepithet <chr>,
#> # bibliographiccitation <chr>, family <chr>, countrycode <chr>,
#> # geodeticdatum <chr>, coordinateuncertaintyinmeters <chr>,
#> # highergeography <chr>, continent <chr>, verbatimlocality <chr>,
#> # day <chr>, kingdom <chr>, collectioncode <chr>,
#> # occurrencestatus <chr>, coordinateprecision <chr>,
#> # institutioncode <chr>, scientificname <chr>, locality <chr>,
#> # class <chr>, vernacularname <chr>, county <chr>,
#> # decimallatitude <chr>, occurrenceid <chr>, language <chr>,
#> # license <chr>, country <chr>, georeferenceverificationstatus <chr>,
#> # modified <chr>, eventdate <chr>, nomenclaturalcode <chr>,
#> # verbatimeventdate <chr>, genus <chr>, order <chr>,
#> # catalognumber <chr>, enddayofyear <chr>, locationremarks <chr>,
#> # infraspecificepithet <chr>, georeferenceprotocol <chr>,
#> # lifestage <chr>, verbatimlongitude <chr>, recordedby <chr>,
#> # preparations <chr>, scientificnameauthorship <chr>,
#> # georeferencesources <chr>, sex <chr>, verbatimlatitude <chr>,
#> # dynamicproperties <chr>, georeferenceremarks <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, messages = FALSE)
res$data
#> # A tibble: 19 x 74
#> month decimallongitude startdayofyear accessrights kingdom
#> <chr> <chr> <chr> <chr> <chr>
#> 1 12 -100.8276541162 336 http://vertnet.org/resou… Animal…
#> 2 03 -100.9827 64 http://vertnet.org/resou… Animal…
#> 3 1 -100.759483 1 http://www.vertnet.org/r… Animal…
#> 4 3 -100.7373 67 http://biodiversity.ku.e… Animal…
#> 5 11 <NA> 305 http://vertnet.org/resou… Animal…
#> 6 10 <NA> 282 <NA> Animal…
#> 7 8 <NA> 234 <NA> Animal…
#> 8 12 <NA> 342 <NA> Animal…
#> 9 12 <NA> 358 http://www.vertnet.org/r… Animal…
#> 10 1 <NA> 1 http://vertnet.org/resou… Animal…
#> 11 11 <NA> 313 <NA> Animal…
#> 12 9 <NA> 272 <NA> Animal…
#> 13 12 <NA> 335 <NA> Animal…
#> 14 9 <NA> 259 <NA> Animal…
#> 15 10 <NA> 297 <NA> Animal…
#> 16 12 <NA> 339 <NA> Animal…
#> 17 11 <NA> 305 <NA> Animal…
#> 18 11 <NA> 315 <NA> Animal…
#> 19 <NA> <NA> <NA> <NA> Animal…
#> # ... with 69 more variables: verbatimcoordinatesystem <chr>, day <chr>,
#> # identificationverificationstatus <chr>, occurrenceid <chr>,
#> # identificationqualifier <chr>, phylum <chr>, verbatimeventdate <chr>,
#> # coordinateuncertaintyinmeters <chr>, higherclassification <chr>,
#> # sex <chr>, year <chr>, specificepithet <chr>, basisofrecord <chr>,
#> # geodeticdatum <chr>, occurrenceremarks <chr>, highergeography <chr>,
#> # continent <chr>, scientificname <chr>, language <chr>,
#> # institutionid <chr>, country <chr>, genus <chr>,
#> # georeferenceprotocol <chr>, family <chr>, stateprovince <chr>,
#> # county <chr>, georeferenceddate <chr>, references <chr>,
#> # georeferencedby <chr>, verbatimlocality <chr>, institutioncode <chr>,
#> # organismid <chr>, eventtime <chr>, preparations <chr>,
#> # recordedby <chr>, license <chr>, dynamicproperties <chr>,
#> # georeferenceverificationstatus <chr>, modified <chr>, eventdate <chr>,
#> # individualcount <chr>, bibliographiccitation <chr>,
#> # verbatimcoordinates <chr>, georeferencesources <chr>,
#> # catalognumber <chr>, locationaccordingto <chr>, collectioncode <chr>,
#> # class <chr>, previousidentifications <chr>, decimallatitude <chr>,
#> # locality <chr>, othercatalognumbers <chr>, identifiedby <chr>,
#> # nomenclaturalcode <chr>, order <chr>, enddayofyear <chr>,
#> # minimumelevationinmeters <chr>, associatedoccurrences <chr>,
#> # maximumelevationinmeters <chr>, samplingprotocol <chr>,
#> # dateidentified <chr>, eventremarks <chr>, datasetname <chr>,
#> # locationremarks <chr>, taxonrank <chr>, countrycode <chr>,
#> # occurrencestatus <chr>, vernacularname <chr>, recordnumber <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", messages = FALSE)
res$data
#> # A tibble: 10 x 71
#> month decimallongitude startdayofyear minimumelevation… accessrights
#> <chr> <chr> <chr> <chr> <chr>
#> 1 10 -119.582 288 1780 http://vertnet…
#> 2 10 -119.582 288 1780 http://vertnet…
#> 3 06 -116.99451 159 1481.328 http://www.ver…
#> 4 10 -119.582 288 1780 http://vertnet…
#> 5 10 -119.582 288 1780 http://vertnet…
#> 6 10 -119.582 288 1780 http://vertnet…
#> 7 10 -119.582 288 1780 http://vertnet…
#> 8 06 -114.09658 165 2072.64 http://www.ver…
#> 9 09 -118.57885 248 1786.128 http://www.ver…
#> 10 06 -116.99451 159 1481.328 http://www.ver…
#> # ... with 66 more variables: kingdom <chr>,
#> # verbatimcoordinatesystem <chr>, day <chr>,
#> # identificationverificationstatus <chr>, occurrenceid <chr>,
#> # identificationqualifier <chr>, phylum <chr>, verbatimeventdate <chr>,
#> # coordinateuncertaintyinmeters <chr>, higherclassification <chr>,
#> # lifestage <chr>, modified <chr>, year <chr>, specificepithet <chr>,
#> # basisofrecord <chr>, geodeticdatum <chr>, highergeography <chr>,
#> # continent <chr>, scientificname <chr>, catalognumber <chr>,
#> # language <chr>, institutionid <chr>, country <chr>, genus <chr>,
#> # georeferenceprotocol <chr>, family <chr>, stateprovince <chr>,
#> # county <chr>, georeferenceddate <chr>, references <chr>,
#> # georeferencedby <chr>, verbatimlocality <chr>, habitat <chr>,
#> # institutioncode <chr>, organismid <chr>,
#> # maximumelevationinmeters <chr>, preparations <chr>, recordedby <chr>,
#> # sex <chr>, license <chr>, dynamicproperties <chr>,
#> # georeferenceverificationstatus <chr>, infraspecificepithet <chr>,
#> # samplingprotocol <chr>, eventdate <chr>, individualcount <chr>,
#> # bibliographiccitation <chr>, verbatimcoordinates <chr>,
#> # georeferencesources <chr>, dateidentified <chr>,
#> # locationaccordingto <chr>, collectioncode <chr>, class <chr>,
#> # previousidentifications <chr>, decimallatitude <chr>, locality <chr>,
#> # othercatalognumbers <chr>, identifiedby <chr>,
#> # nomenclaturalcode <chr>, order <chr>, enddayofyear <chr>,
#> # locationremarks <chr>, recordnumber <chr>, collectionid <chr>,
#> # associatedmedia <chr>, occurrenceremarks <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, messages = FALSE)
res$data
#> # A tibble: 10 x 60
#> month decimallongitude startdayofyear minimumelevation… accessrights
#> <chr> <chr> <chr> <chr> <chr>
#> 1 07 -105.68633 193 2182.368 http://vertnet…
#> 2 07 -105.705479 196 2023.872 http://vertnet…
#> 3 07 -105.705479 196 2023.872 http://vertnet…
#> 4 07 -105.705479 196 2023.872 http://vertnet…
#> 5 07 -105.705479 196 2023.872 http://vertnet…
#> 6 07 -105.705479 196 2023.872 http://vertnet…
#> 7 07 -105.705479 196 2023.872 http://vertnet…
#> 8 07 -105.705479 196 2023.872 http://vertnet…
#> 9 07 -105.705479 196 2023.872 http://vertnet…
#> 10 07 -105.705479 196 2023.872 http://vertnet…
#> # ... with 55 more variables: kingdom <chr>, day <chr>,
#> # identificationverificationstatus <chr>, occurrenceid <chr>,
#> # identificationqualifier <chr>, phylum <chr>, verbatimeventdate <chr>,
#> # coordinateuncertaintyinmeters <chr>, higherclassification <chr>,
#> # sex <chr>, year <chr>, specificepithet <chr>, basisofrecord <chr>,
#> # geodeticdatum <chr>, occurrenceremarks <chr>, highergeography <chr>,
#> # continent <chr>, scientificname <chr>, language <chr>,
#> # institutionid <chr>, country <chr>, genus <chr>,
#> # georeferenceprotocol <chr>, family <chr>, stateprovince <chr>,
#> # county <chr>, georeferenceddate <chr>, references <chr>,
#> # georeferencedby <chr>, verbatimlocality <chr>, institutioncode <chr>,
#> # organismid <chr>, maximumelevationinmeters <chr>, preparations <chr>,
#> # recordedby <chr>, dynamicproperties <chr>,
#> # georeferenceverificationstatus <chr>, modified <chr>, eventdate <chr>,
#> # individualcount <chr>, bibliographiccitation <chr>,
#> # georeferencesources <chr>, catalognumber <chr>,
#> # locationaccordingto <chr>, recordnumber <chr>, class <chr>,
#> # previousidentifications <chr>, decimallatitude <chr>, locality <chr>,
#> # othercatalognumbers <chr>, identifiedby <chr>,
#> # nomenclaturalcode <chr>, enddayofyear <chr>, order <chr>,
#> # collectioncode <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 57
#> higherclassification stateprovince basisofrecord month decimallongitude
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Animalia | Chordata… California PreservedSpe… 2 -121.7833
#> 2 Animalia | Chordata… California PreservedSpe… 6 -122.15
#> 3 Animalia | Chordata… California PreservedSpe… 5 -120.9014
#> 4 Animalia; Chordata;… South Caroli… PreservedSpe… 2 -79.86151
#> 5 Animalia; Chordata;… California PreservedSpe… 1 -121.93300
#> 6 Animalia; Chordata;… California PreservedSpe… 1 -121.93300
#> 7 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> 8 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> 9 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> 10 Animalia; Chordata;… California PreservedSpe… 7 -121.85760
#> # ... with 52 more variables: phylum <chr>, references <chr>, year <chr>,
#> # startdayofyear <chr>, taxonrank <chr>, specificepithet <chr>,
#> # bibliographiccitation <chr>, family <chr>, countrycode <chr>,
#> # geodeticdatum <chr>, coordinateuncertaintyinmeters <chr>,
#> # highergeography <chr>, continent <chr>, verbatimlocality <chr>,
#> # day <chr>, kingdom <chr>, collectioncode <chr>,
#> # occurrencestatus <chr>, coordinateprecision <chr>,
#> # institutioncode <chr>, scientificname <chr>, locality <chr>,
#> # class <chr>, vernacularname <chr>, county <chr>,
#> # decimallatitude <chr>, occurrenceid <chr>, language <chr>,
#> # license <chr>, country <chr>, georeferenceverificationstatus <chr>,
#> # modified <chr>, eventdate <chr>, nomenclaturalcode <chr>,
#> # verbatimeventdate <chr>, genus <chr>, order <chr>,
#> # catalognumber <chr>, enddayofyear <chr>, locationremarks <chr>,
#> # infraspecificepithet <chr>, georeferenceprotocol <chr>,
#> # lifestage <chr>, verbatimlongitude <chr>, recordedby <chr>,
#> # verbatimlatitude <chr>, preparations <chr>,
#> # scientificnameauthorship <chr>, georeferenceremarks <chr>, sex <chr>,
#> # georeferencesources <chr>, dynamicproperties <chr>
Limit the number of records returned (under 1000)
res <- vertsearch("(kansas state OR KSU)", limit = 200)
res$data
#> # A tibble: 200 x 78
#> individualcount georeferenceprot… recordedby bibliographiccitation
#> <chr> <chr> <chr> <chr>
#> 1 8 GEOLocate (Rios … H. W. Robi… Academy of Natural Scien…
#> 2 11 GEOLocate (Rios … H. W. Robi… Academy of Natural Scien…
#> 3 3 GEOLocate (Rios … H. W. Robi… Academy of Natural Scien…
#> 4 <NA> <NA> <NA> California Academy of Sc…
#> 5 <NA> <NA> <NA> California Academy of Sc…
#> 6 <NA> <NA> <NA> California Academy of Sc…
#> 7 1 VertNet Georefer… MCCOY, C J… Carnegie Museum of Natur…
#> 8 1 VertNet Georefer… MCCOY, C J… Carnegie Museum of Natur…
#> 9 1 VertNet Georefer… MCCOY, C J… Carnegie Museum of Natur…
#> 10 1 VertNet Georefer… MCCOY, C J… Carnegie Museum of Natur…
#> # ... with 190 more rows, and 74 more variables: stateprovince <chr>,
#> # basisofrecord <chr>, month <chr>, decimallongitude <chr>,
#> # phylum <chr>, references <chr>, georeferencedby <chr>, year <chr>,
#> # taxonrank <chr>, specificepithet <chr>, family <chr>,
#> # countrycode <chr>, locality <chr>, geodeticdatum <chr>,
#> # coordinateuncertaintyinmeters <chr>, highergeography <chr>,
#> # continent <chr>, day <chr>, kingdom <chr>, georeferenceddate <chr>,
#> # footprintwkt <chr>, institutioncode <chr>, scientificname <chr>,
#> # preparations <chr>, disposition <chr>, class <chr>,
#> # identificationremarks <chr>, county <chr>, decimallatitude <chr>,
#> # occurrenceid <chr>, language <chr>, license <chr>, country <chr>,
#> # georeferenceverificationstatus <chr>, othercatalognumbers <chr>,
#> # infraspecificepithet <chr>, eventdate <chr>, identifiedby <chr>,
#> # nomenclaturalcode <chr>, fieldnumber <chr>, verbatimeventdate <chr>,
#> # genus <chr>, order <chr>, catalognumber <chr>, collectioncode <chr>,
#> # higherclassification <chr>, lifestage <chr>, startdayofyear <chr>,
#> # occurrenceremarks <chr>, verbatimlocality <chr>,
#> # georeferencesources <chr>, verbatimcoordinatesystem <chr>,
#> # institutionid <chr>, modified <chr>, dateidentified <chr>,
#> # enddayofyear <chr>, georeferenceremarks <chr>, accessrights <chr>,
#> # occurrencestatus <chr>, sex <chr>, establishmentmeans <chr>,
#> # identificationverificationstatus <chr>, identificationqualifier <chr>,
#> # organismid <chr>, dynamicproperties <chr>, verbatimcoordinates <chr>,
#> # locationaccordingto <chr>, recordnumber <chr>,
#> # previousidentifications <chr>, samplingprotocol <chr>,
#> # minimumelevationinmeters <chr>, maximumelevationinmeters <chr>,
#> # datasetname <chr>, collectionid <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 messages=TRUE to get helpful messages - messages=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, messages = TRUE)