rvertnet
Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Retrieve, map and summarize data from the 'VertNet.org' archives (< http://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
rvertnet is a client for interacting with VertNet.org.
VertNet.org API docs: https://github.com/VertNet/webapp/wiki/The-API-search-function
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 = "[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, 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.
News
rvertnet 0.7.0
BUG FIXES
- add month and day params to
searchbyterm(#64)
rvertnet 0.6.2
BUG FIXES
- A small data source used in one function was on the web, and was moved - that data source now within the pkg as quite small, and now pkg won't break when the file is moved again (#61) (#62)
rvertnet 0.6.0
Added Code of Conduct.
NEW FEATURES
- Now using
crulpackage for HTTP requests instead ofhttr(#57) - Note that
verboseparameter has been replaced withmessagesthroughout the package. - Now with function for search for trait data:
traitsearch()(#55)
DEFUNCT AND DEPRECATED
- All
dumpfunctions are now defunct. Those functions tried to help users work with bulk Vertnet data - the setup has gotten too complex (#56)
MINOR IMPROVEMENTS
- Improvements to documentation for
traitsearch()function on what fields have given data (#58) thanks @gaurav vertsearch()andsearchbyterm()gain new parameteronly_dwc, which allows to optionally only return Darwin Core fields
BUG FIXES
- Small fix to
vertsummary()(#59)
rvertnet 0.5.0
NEW FEATURES
searchbyterm()gains new parameterqueryto allow full text search, much likevertsearch(), but with the ability to also use all the parameters available insearchbyterm()(#53)
MINOR IMPROVEMENTS
- Use
dplyr::bind_rowsinstead of the deprecateddplyr::rbind_all(#51) - remove personal email address from tests (#52)
- Namespace base R pkg fxn calls (
methods/stats/utils), and removed some package dependencies that we didn't really need (plyr) (#54)
rvertnet 0.4.4
MINOR IMPROVEMENTS
- Updated docs to better indicate how to use the cursor feature (#49)
- Now using explicit encoding specification when using
httr::content()(#47)
BUG FIXES
- Fixed
externalptrerror in the internalvert_GET()function (#48)
rvertnet 0.4.1
BUG FIXES
- Fixed a bug in
bigsearch()in which we had forgotten to do internal conversion of logical input to 0/1 needed by the web API (#46)
rvertnet 0.4.0
NEW FEATURES
- New set of functions to make working with VertNet data dumps
easier.
dump_links()gives you links to various data dump resources;dump_init()initialized a SQLite database connection;dump_tbl()creates adplyr::tblobject, which can then be used in adplyrquery. This setup requires that the user manually download data dumps uncompress, and load into SQLite. We hope to make this process easier in the future. (#36)
MINOR IMPROVEMENTS
- Fixes to
vertmap()for newggplot2version (#43) - Added note to docs for
bigsearch()for how to read in data after obtaining the data (#44)
BUG FIXES
- Fix to the
searchbyterm()function. When the parameterstateprovincewas used, lead to error, as that param requires different handling than other params. (#45)
rvertnet 0.3.4
NEW FEATURES
- New function
vert_id()to get occurrence records by occurenceid, that is, single occurrence ids. (#40)
MINOR IMPROVEMENTS
- Explicitly import non-base R functions (#39)
BUG FIXES
- Lowercase
occurenceIDtooccurrenceidto simplify life (#41)
rvertnet 0.3.0
NEW FEATURES
searchbyterm()andbigsearch()have some parameters that accept multiple values. Fixed to allow this (#37)- Internals of
searchbyterm(),spatialsearch(), andvertsearch()reworked to use cursor so we internally do paging for you for bigger result sets. (#25)
MINOR IMPROVEMENTS
- Replaced
data.tableimport withdplyr - Using
skip_on_cran()(#38) - Minor vignette updates (#35)
- Metadata now returned in data requests (#33)
rvertnet 0.2.2
Package completely reworked for the new VertNet API.
NEW FEATURES
- The functions
vertavailablemaps(),vertlocations(),vertoccurrence(),vertoccurrencecount(),vertproviders(),verttaxa()are now defunct. You can call these functions, but they print an error message, saying they are defunct. - Gained new functions
bigsearch(),searchbyterm(),spatialsearch(), andvertsummary(). - Gained new author: Chris Ray
MINOR IMPROVEMENTS
RJSONIOreplaced withjsonlite- Changed from CC0 to MIT license
rvertnet 0.0-5
NEW FEATURES
- released to CRAN