rvertnet introduction

rvertnet is a client for interacting with VertNet.org.

Installation

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 by term

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] "2016-09-23T18:59:51.449530"
#> 
#> $response_records
#> [1] 10
#> 
#> $request_origin
#> [1] "45.523452,-122.676207"
#> 
#> $last_cursor
#> [1] "False:CqAFCuwCCr4C9wAAABn_____jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87L0s_N0s7Onv8AAP90baCgmYuMoKD_AAD_XZ6Pj5qRmJaRmv8AAP9zdG2WkZuah_8AAP9dm4ic_wAA_3N0bZuQnKCWm_8AAP9dnIqSidCdlo2b0oyPmpyWkpqRjNDKz8zPx_8AAP9zf5yKkonQnZaNm9KMj5qclpKakYzQys_Mz8f_AAD__wD-__6MgYmajYuRmovSj5CNi56T3paRm5qH0s3PzsvSz83Szs6e_wB0baCgmYuMoKD_AF2ej4-akZiWkZr_AHN0bZaRm5qH_wBdm4ic_wBzdG2bkJyglpv_AF2cipKJ0J2WjZvSjI-anJaSmpGM0MrPzM_H_wBzf5yKkonQnZaNm9KMj5qclpKakYzQys_Mz8f_AP_-EAohBN0EkB08Gxk5AAAAAOb___9IClAAWgsJaEr43cr5mgoQAmCrk_-KBBINRG9jdW1lbnRJbmRleBr9AShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxNC0wMi0xMWEiKSAoSVMgImluZGV4X25hbWUiICJkd2MiKSAoQU5EIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKE9SIChJUyAicmF0b21fc3RhdGVwcm92aW5jZSIgImNhbGlmb3JuaWEiKSAoUVQgIkNhbGlmb3JuaWEiICJydGV4dF9zdGF0ZXByb3ZpbmNlIikpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#> 
#> $limit
#> [1] 10
#> 
#> $query_version
#> [1] "search.py 2015-08-29T21:04:44+02:00"
#> 
#> $matching_records
#> [1] ">10000"
#> 
#> $api_version
#> [1] "api.py 2015-09-02T11:09:38+02:00"

The data

res$data
#> # A tibble: 10 × 68
#>                 modified language                            accessrights
#>                    <chr>    <chr>                                   <chr>
#> 1             2015-01-06       en                                    <NA>
#> 2             2015-01-06       en                                    <NA>
#> 3  2015-05-11 07:55:08.0       en http://vertnet.org/resources/norms.html
#> 4  2015-05-11 07:55:08.0       en http://vertnet.org/resources/norms.html
#> 5  2015-08-26 13:10:07.0       en http://vertnet.org/resources/norms.html
#> 6  2015-08-26 13:10:07.0       en http://vertnet.org/resources/norms.html
#> 7  2015-08-26 13:10:07.0       en http://vertnet.org/resources/norms.html
#> 8  2015-08-26 13:10:07.0       en http://vertnet.org/resources/norms.html
#> 9  2015-08-26 13:10:07.0       en http://vertnet.org/resources/norms.html
#> 10 2015-08-26 13:10:07.0       en http://vertnet.org/resources/norms.html
#> # ... with 65 more variables: references <chr>, institutionid <chr>,
#> #   institutioncode <chr>, collectioncode <chr>, basisofrecord <chr>,
#> #   dynamicproperties <chr>, occurrenceid <chr>, catalognumber <chr>,
#> #   recordedby <chr>, individualcount <chr>, sex <chr>,
#> #   establishmentmeans <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>,
#> #   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 × 71
#>                 modified language
#>                    <chr>    <chr>
#> 1  2010-01-14 13:06:23.0       en
#> 2  2011-11-17 12:02:57.0       en
#> 3             2013-08-07       en
#> 4  2015-04-14 15:45:27.0       en
#> 5  2015-04-17 17:39:57.0       en
#> 6  2015-08-18 10:24:17.0       en
#> 7             2016-06-02       en
#> 8                   <NA>     <NA>
#> 9                   <NA>     <NA>
#> 10                  <NA>     <NA>
#> 11                  <NA>     <NA>
#> 12                  <NA>     <NA>
#> 13                  <NA>     <NA>
#> 14                  <NA>     <NA>
#> 15                  <NA>     <NA>
#> 16                  <NA>     <NA>
#> 17                  <NA>     <NA>
#> 18                  <NA>     <NA>
#> 19                  <NA>     <NA>
#> # ... with 69 more variables: accessrights <chr>, references <chr>,
#> #   institutionid <chr>, institutioncode <chr>, collectioncode <chr>,
#> #   datasetname <chr>, basisofrecord <chr>, dynamicproperties <chr>,
#> #   occurrenceid <chr>, catalognumber <chr>, recordedby <chr>,
#> #   individualcount <chr>, sex <chr>, establishmentmeans <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: 2 × 66
#>                modified language
#>                   <chr>    <chr>
#> 1 2013-01-05 17:46:29.0       en
#> 2 2015-06-22 12:58:04.0       en
#> # ... with 64 more variables: accessrights <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>,
#> #   establishmentmeans <chr>, preparations <chr>, associatedmedia <chr>,
#> #   othercatalognumbers <chr>, occurrenceremarks <chr>, organismid <chr>,
#> #   previousidentifications <chr>, eventdate <chr>, enddayofyear <chr>,
#> #   year <chr>, month <chr>, day <chr>, verbatimeventdate <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

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 × 69
#>                 modified language
#>                    <chr>    <chr>
#> 1  2013-09-10 12:55:00.0       en
#> 2  2013-09-10 12:55:00.0       en
#> 3  2013-09-10 12:55:00.0       en
#> 4  2014-01-14 16:04:11.0       en
#> 5  2014-06-03 17:37:34.0       en
#> 6  2014-09-09 14:04:14.0       en
#> 7  2014-09-09 14:04:14.0       en
#> 8  2015-08-03 19:48:08.0       en
#> 9  2015-09-08 00:33:35.0       en
#> 10                  <NA>       en
#> # ... with 67 more variables: accessrights <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>, establishmentmeans <chr>, occurrencestatus <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>, 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>, 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>,
#> #   nomenclaturalcode <chr>

Global full text search

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 × 57
#>      modified language                            accessrights
#>         <chr>    <chr>                                   <chr>
#> 1  2015-01-06       en                                    <NA>
#> 2  2015-01-06       en                                    <NA>
#> 3  2015-10-13       en http://vertnet.org/resources/norms.html
#> 4  2015-10-13       en http://vertnet.org/resources/norms.html
#> 5  2015-10-13       en http://vertnet.org/resources/norms.html
#> 6  2015-10-13       en http://vertnet.org/resources/norms.html
#> 7  2015-10-13       en http://vertnet.org/resources/norms.html
#> 8  2015-10-13       en http://vertnet.org/resources/norms.html
#> 9  2015-10-13       en http://vertnet.org/resources/norms.html
#> 10 2015-10-13       en http://vertnet.org/resources/norms.html
#> # ... with 54 more variables: references <chr>, institutionid <chr>,
#> #   institutioncode <chr>, collectioncode <chr>, basisofrecord <chr>,
#> #   dynamicproperties <chr>, occurrenceid <chr>, catalognumber <chr>,
#> #   recordedby <chr>, sex <chr>, establishmentmeans <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>, 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 × 76
#>              modified language
#>                 <chr>    <chr>
#> 1  2008-09-03 0:00:00       en
#> 2  2008-09-03 0:00:00       en
#> 3  2008-09-03 0:00:00       en
#> 4  2008-09-03 0:00:00       en
#> 5  2008-09-03 0:00:00       en
#> 6  2008-09-03 0:00:00       en
#> 7  2008-09-03 0:00:00       en
#> 8  2008-09-03 0:00:00       en
#> 9  2008-09-03 0:00:00       en
#> 10 2008-09-03 0:00:00       en
#> # ... with 190 more rows, and 74 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>,
#> #   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>, verbatimelevation <chr>,
#> #   locationaccordingto <chr>, decimallatitude <chr>,
#> #   decimallongitude <chr>, geodeticdatum <chr>,
#> #   coordinateuncertaintyinmeters <chr>, verbatimcoordinates <chr>,
#> #   verbatimlatitude <chr>, verbatimcoordinatesystem <chr>,
#> #   georeferencedby <chr>, georeferenceddate <chr>,
#> #   georeferenceprotocol <chr>, georeferencesources <chr>,
#> #   georeferenceverificationstatus <chr>, georeferenceremarks <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>,
#> #   nomenclaturalcode <chr>

Pass output of vertsearch() to a map

out <- vertsearch(tax = "(mustela nivalis OR mustela erminea)")
#> Error in vert_GET(fxn, args, lim, verbose, ...): Internal Server Error (HTTP 500).
vertmap(out)
#> Error in match(x, table, nomatch = 0L): object 'out' not found

Lots of data

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.

Email dump of data

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.

Messages

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)