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
remotes::install_github("ropensci/rvertnet")
Search by term
Search for Aves in the state of California, limit to 10 records
res <- searchbyterm(class = "Aves", stateprovince = "California", limit = 10, messages = FALSE)
Inspect metadata
res$meta #> $request_date #> [1] "2020-01-29T02:10:34.011754" #> #> $response_records #> [1] 10 #> #> $submitted_query #> [1] "class:Aves stateprovince:California" #> #> $request_origin #> [1] "45.505106,-122.675026" #> #> $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___9IClAAWgsJqvR3VAbTv8MQA2C9iLGbBBINRG9jdW1lbnRJbmRleBruAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKE9SIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKElTICJyYXRvbV9jbGFzcyIgImF2ZXMiKSkgKFFUICJDYWxpZm9ybmlhIiAicnRleHRfc3RhdGVwcm92aW5jZSIpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH" #> #> $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; Aves;… California PreservedSpe… 1 -121.93300 #> 5 Animalia; Chordata; Aves;… California PreservedSpe… 1 -121.93300 #> 6 Animalia; Chordata; Aves;… California PreservedSpe… 7 -121.85760 #> 7 Animalia; Chordata; Aves;… California PreservedSpe… 7 -121.85760 #> 8 Animalia; Chordata; Aves;… California PreservedSpe… 7 -121.85760 #> 9 Animalia; Chordata; Aves;… California PreservedSpe… 7 -121.85760 #> 10 Animalia; Chordata; Aves;… California PreservedSpe… 6 -121.85760
Search for Mustela nigripes in the states of Wyoming or South Dakota, limit to 20 records
res <- searchbyterm(specificepithet = "nigripes", stateprovince = "(wyoming OR south dakota)", limit = 20, messages = FALSE) res$data[,1:5] #> # A tibble: 20 x 5 #> month decimallongitude startdayofyear accessrights kingdom #> <chr> <chr> <chr> <chr> <chr> #> 1 12 -100.8276541162 336 http://vertnet.org/resources/n… Animal… #> 2 03 -100.9827 64 http://vertnet.org/resources/n… Animal… #> 3 1 -100.759483 1 http://vertnet.org/resources/n… Animal… #> 4 3 -100.7373 67 http://biodiversity.ku.edu/res… Animal… #> 5 11 <NA> 305 http://vertnet.org/resources/n… Animal… #> 6 10 <NA> 282 <NA> Animal… #> 7 8 <NA> 234 <NA> Animal… #> 8 12 <NA> 342 <NA> Animal… #> 9 12 <NA> 358 http://www.vertnet.org/resourc… Animal… #> 10 1 <NA> 1 http://vertnet.org/resources/n… Animal… #> 11 1 <NA> 1 http://vertnet.org/resources/n… Animal… #> 12 11 <NA> 313 <NA> Animal… #> 13 9 <NA> 272 <NA> Animal… #> 14 12 <NA> 335 <NA> Animal… #> 15 9 <NA> 259 <NA> Animal… #> 16 10 <NA> 297 <NA> Animal… #> 17 12 <NA> 339 <NA> Animal… #> 18 11 <NA> 305 <NA> Animal… #> 19 11 <NA> 315 <NA> Animal… #> 20 <NA> <NA> <NA> http://vertnet.org/resources/n… Animal…
dplyr downstream
You can pass the data object directly on to dplyr functions. Here, we get a table of record counts by species in descending order.
library("dplyr") out <- searchbyterm(genus = "Ochotona", limit = 800) out$data %>% group_by(scientificname) %>% summarise(count = length(scientificname)) %>% arrange(desc(count)) #> # A tibble: 20 x 2 #> scientificname count #> <chr> <int> #> 1 Ochotona princeps 450 #> 2 Ochotona pallasi 129 #> 3 Ochotona princeps saxatilis 103 #> 4 Ochotona hyperborea 30 #> 5 Ochotona dauurica 21 #> 6 Ochotona collaris 15 #> 7 Ochotona princeps figginsi 14 #> 8 Ochotona princeps taylori 8 #> 9 Ochotona princeps schisticeps 6 #> 10 Ochotona alpina 4 #> 11 Ochotona princeps muiri 4 #> 12 Ochotona hyperborea mantchurica 3 #> 13 Ochotona princeps incana 3 #> 14 Ochotona princeps princeps 3 #> 15 Ochotona princeps murri 2 #> 16 Ochotona princeps brunnescens 1 #> 17 Ochotona princeps jewetti 1 #> 18 Ochotona princeps tutelata 1 #> 19 Ochotona princeps uinta 1 #> 20 Ochotona princeps ventorum 1
Big 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", rfile = "pikaRecords", email = "[email protected]@search.luv") #> Processing request... #> #> Download of records file 'mydata' requested for '[email protected]' #> #> Query/URL: "http://api.vertnet-portal.appspot.com/api/download?q=%7B%22q%22:%22genus:ochotona%22,%22n%22:%22mydata%22,%22e%22:%[email protected]%22%7D" #> #> Thank you! Download instructions will be sent by email.
Spatial search
res <- spatialsearch(lat = 33.529, long = -105.694, radius = 2000, limit = 10, messages = FALSE) res$data[,1:5] #> # A tibble: 10 x 5 #> month decimallongitude startdayofyear minimumelevationin… accessrights #> <chr> <chr> <chr> <chr> <chr> #> 1 07 -105.68633 193 2182.368 http://vertnet.org… #> 2 07 -105.705479 196 2023.872 http://vertnet.org… #> 3 07 -105.705479 196 2023.872 http://vertnet.org… #> 4 07 -105.705479 196 2023.872 http://vertnet.org… #> 5 07 -105.705479 196 2023.872 http://vertnet.org… #> 6 07 -105.705479 196 2023.872 http://vertnet.org… #> 7 07 -105.705479 196 2023.872 http://vertnet.org… #> 8 07 -105.705479 196 2023.872 http://vertnet.org… #> 9 07 -105.705479 196 2023.872 http://vertnet.org… #> 10 07 -105.705479 196 2023.872 http://vertnet.org…
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 package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.