rvertnet
rvertnet is a client for interacting with VertNet.org.
VertNet.org API docs: https://github.com/VertNet/webapp/wiki/The-API-search-function
Installation
Stable CRAN version
install.packages("rvertnet")Or development version from GitHub
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", lim = 10, verbose = FALSE)Inspect metadata
res$meta
#> $request_date
#> [1] "2017-08-14T21:55:09.833740"
#>
#> $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-19FzJ8QAmDc4-iNBRINRG9jdW1lbnRJbmRleBruAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKE9SIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKElTICJyYXRvbV9jbGFzcyIgImF2ZXMiKSkgKFFUICJDYWxpZm9ybmlhIiAicnRleHRfc3RhdGVwcm92aW5jZSIpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#>
#> $query_version
#> [1] "search.py 2016-08-15T16:43+02:00"
#>
#> $matching_records
#> [1] ">10000"
#>
#> $api_version
#> [1] "api.py 2017-01-12T20:08-03:00"Inspect data. A dplyr data.frame is given back, so you get a nice brief data summary:
res$data[,1:5]
#> # A tibble: 10 x 5
#> 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 2 more variables: accessrights <chr>,
#> # bibliographiccitation <chr>Search for Mustela nigripes in the states of Wyoming or South Dakota, limit to 20 records
res <- searchbyterm(specificepithet = "nigripes", state = "(wyoming OR south dakota)", limit = 20, verbose = FALSE)
res$data[,1:5]
#> # A tibble: 19 x 5
#> modified language license
#> <chr> <chr> <chr>
#> 1 2010-01-14 13:06:23.0 en CC-BY
#> 2 2011-11-17 12:02:57.0 en CC0
#> 3 2013-08-07 en <NA>
#> 4 2015-11-23 09:17:09.0 en CC0
#> 5 2016-02-01 17:40:23.0 en CC0
#> 6 2016-04-12 00:24:00.0 en CC0
#> 7 2016-11-15 en CC0
#> 8 <NA> <NA> CC0
#> 9 <NA> <NA> CC0
#> 10 <NA> <NA> CC0
#> 11 <NA> <NA> CC0
#> 12 <NA> <NA> CC0
#> 13 <NA> <NA> CC0
#> 14 <NA> <NA> CC0
#> 15 <NA> <NA> CC0
#> 16 <NA> <NA> CC0
#> 17 <NA> <NA> CC0
#> 18 <NA> <NA> CC0
#> 19 <NA> <NA> CC0
#> # ... with 2 more variables: accessrights <chr>,
#> # bibliographiccitation <chr>dplyr downstream
You can pass the data object directly on to dplyr functions. Here, we get a table of record counts by species in descending order.
library("dplyr")
out <- searchbyterm(genus = "Ochotona", limit = 800)
out$data %>%
group_by(scientificname) %>%
summarise(count = length(scientificname)) %>%
arrange(desc(count))
#> # A tibble: 28 x 2
#> scientificname count
#> <chr> <int>
#> 1 Ochotona princeps 284
#> 2 Ochotona princeps saxatilis 202
#> 3 Ochotona pallasi 132
#> 4 Ochotona princeps muiri 43
#> 5 Ochotona hyperborea 39
#> 6 Ochotona dauurica 21
#> 7 Ochotona (Pika) princeps Richardson, 1828 20
#> 8 Ochotona princeps figginsi 13
#> 9 Ochotona princeps nevadensis 8
#> 10 Ochotona alpina 4
#> # ... with 18 more rowsBig data
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", rf = "pikaRecords", email = "big@@search.luv")
#> 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.Spatial search
res <- spatialsearch(lat = 33.529, lon = -105.694, radius = 2000, limit = 10, verbose = FALSE)
res$data[,1:5]
#> # A tibble: 10 x 5
#> 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 2 more variables: bibliographiccitation <chr>, references <chr>Contributors
- Scott Chamberlain @sckott
- Chris Ray @Pika8tona
- Vijay Barve @vijaybarve
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rvertnetin R doingcitation(package = 'rvertnet') - 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.