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, messages = FALSE)Inspect metadata
res$meta
#> $request_date
#> [1] "2018-04-17T06:11:10.584520"
#>
#> $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___9IClAAWgsJdSRwg5uy6lIQAmDOz46YAhINRG9jdW1lbnRJbmRleBruAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKE9SIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKElTICJyYXRvbV9jbGFzcyIgImF2ZXMiKSkgKFFUICJDYWxpZm9ybmlhIiAicnRleHRfc3RhdGVwcm92aW5jZSIpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#>
#> $query_version
#> [1] "search.py 2016-08-15T16:43+02:00"
#>
#> $matching_records
#> [1] ">10000"
#>
#> $api_version
#> [1] "api.py 2017-11-24T12:16-03:00"Inspect data. A dplyr data.frame is given back, so you get a nice brief data summary:
res$data[,1:5]
#> # A tibble: 10 x 5
#> 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 -121.85760Search 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, messages = FALSE)
res$data[,1:5]
#> # A tibble: 19 x 5
#> month decimallongitude startdayofyear accessrights kingdom
#> <chr> <chr> <chr> <chr> <chr>
#> 1 12 -100.8276541162 336 http://vertnet.org/resou… Animal…
#> 2 03 -100.9827 64 http://vertnet.org/resou… Animal…
#> 3 1 -100.759483 1 http://www.vertnet.org/r… Animal…
#> 4 3 -100.7373 67 http://biodiversity.ku.e… Animal…
#> 5 11 <NA> 305 http://vertnet.org/resou… Animal…
#> 6 10 <NA> 282 <NA> Animal…
#> 7 8 <NA> 234 <NA> Animal…
#> 8 12 <NA> 342 <NA> Animal…
#> 9 12 <NA> 358 http://www.vertnet.org/r… Animal…
#> 10 1 <NA> 1 http://vertnet.org/resou… Animal…
#> 11 11 <NA> 313 <NA> Animal…
#> 12 9 <NA> 272 <NA> Animal…
#> 13 12 <NA> 335 <NA> Animal…
#> 14 9 <NA> 259 <NA> Animal…
#> 15 10 <NA> 297 <NA> Animal…
#> 16 12 <NA> 339 <NA> Animal…
#> 17 11 <NA> 305 <NA> Animal…
#> 18 11 <NA> 315 <NA> Animal…
#> 19 <NA> <NA> <NA> <NA> Animal…dplyr downstream
You can pass the data object directly on to dplyr functions. Here, we get a table of record counts by species in descending order.
library("dplyr")
out <- searchbyterm(genus = "Ochotona", limit = 800)
out$data %>%
group_by(scientificname) %>%
summarise(count = length(scientificname)) %>%
arrange(desc(count))
#> # A tibble: 23 x 2
#> scientificname count
#> <chr> <int>
#> 1 Ochotona princeps 428
#> 2 Ochotona pallasi 129
#> 3 Ochotona princeps saxatilis 103
#> 4 Ochotona hyperborea 30
#> 5 Ochotona dauurica 21
#> 6 Ochotona (Pika) princeps Richardson, 1828 20
#> 7 Ochotona collaris 15
#> 8 Ochotona princeps figginsi 14
#> 9 Ochotona princeps schisticeps 6
#> 10 Ochotona princeps taylori 5
#> # ... with 13 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, messages = FALSE)
res$data[,1:5]
#> # A tibble: 10 x 5
#> 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…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.