rvertnet
rvertnet is a client for interacting with VertNet.org.
VertNet.org API docs: 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] "2016-09-23T18:55:14.650960"
#>
#> $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___9IClAAWgsJaEr43cr5mgoQAmD9lv66BBINRG9jdW1lbnRJbmRleBr9AShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxNC0wMi0xMWEiKSAoSVMgImluZGV4X25hbWUiICJkd2MiKSAoQU5EIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKE9SIChJUyAicmF0b21fc3RhdGVwcm92aW5jZSIgImNhbGlmb3JuaWEiKSAoUVQgIkNhbGlmb3JuaWEiICJydGV4dF9zdGF0ZXByb3ZpbmNlIikpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#>
#> $limit
#> [1] 10
#>
#> $query_version
#> [1] "search.py 2015-08-29T21:04:44+02:00"
#>
#> $matching_records
#> [1] ">10000"
#>
#> $api_version
#> [1] "api.py 2015-09-02T11:09:38+02:00"Inspect data. A dplyr data.frame is given back, so you get a nice brief data summary:
res$data[,1:5]
#> # A tibble: 10 × 5
#> 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 2 more variables: references <chr>, institutionid <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$data[,1:5]
#> # A tibble: 19 × 5
#> modified language
#> <chr> <chr>
#> 1 2010-01-14 13:06:23.0 en
#> 2 2011-11-17 12:02:57.0 en
#> 3 2013-08-07 en
#> 4 2015-04-14 15:45:27.0 en
#> 5 2015-04-17 17:39:57.0 en
#> 6 2015-08-18 10:24:17.0 en
#> 7 2016-06-02 en
#> 8 <NA> <NA>
#> 9 <NA> <NA>
#> 10 <NA> <NA>
#> 11 <NA> <NA>
#> 12 <NA> <NA>
#> 13 <NA> <NA>
#> 14 <NA> <NA>
#> 15 <NA> <NA>
#> 16 <NA> <NA>
#> 17 <NA> <NA>
#> 18 <NA> <NA>
#> 19 <NA> <NA>
#> # ... with 3 more variables: accessrights <chr>, references <chr>,
#> # institutionid <chr>dplyr downstream
You can pass the data object directly on to dplyr functions. Here, we get a table of record counts by species in descending order.
library("dplyr")
out <- searchbyterm(genus = "Ochotona", limit = 800)
out$data %>%
group_by(scientificname) %>%
summarise(count = length(scientificname)) %>%
arrange(desc(count))
#> # A tibble: 25 × 2
#> scientificname count
#> <chr> <int>
#> 1 Ochotona princeps 287
#> 2 Ochotona princeps saxatilis 169
#> 3 Ochotona pallasi 114
#> 4 Ochotona princeps muiri 107
#> 5 Ochotona hyperborea 30
#> 6 Ochotona princeps figginsi 18
#> 7 Ochotona dauurica 14
#> 8 Ochotona princeps princeps 9
#> 9 Ochotona princeps brunnescens 8
#> 10 Ochotona princeps cuppes 8
#> # ... with 15 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 × 5
#> 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 3 more variables: accessrights <chr>, references <chr>,
#> # institutionid <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')