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README.md
In rvertnet: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
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
remotes::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", stateprovince = "California",
limit = 10, messages = FALSE)
Inspect metadata
res$meta
#> $request_date
#> [1] "2021-05-12T23:08:19.676358"
#>
#> $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___9IClAAWgsJqvR3VAbTv8MQA2Cl4NG4AhINRG9jdW1lbnRJbmRleBruAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKE9SIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKElTICJyYXRvbV9jbGFzcyIgImF2ZXMiKSkgKFFUICJDYWxpZm9ybmlhIiAicnRleHRfc3RhdGVwcm92aW5jZSIpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#>
#> $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 = "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, long = -105.694, radius = 2000,
limit = 10, messages = FALSE)
res$data[,1:5]
#> # A tibble: 10 x 5
#> month decimallongitude startdayofyear minimumelevationin… accessrights
#> <chr> <chr> <chr> <chr> <chr>
#> 1 07 -105.68633 193 2182.368 http://vertnet.org…
#> 2 07 -105.705479 196 2023.872 http://vertnet.org…
#> 3 07 -105.705479 196 2023.872 http://vertnet.org…
#> 4 07 -105.705479 196 2023.872 http://vertnet.org…
#> 5 07 -105.705479 196 2023.872 http://vertnet.org…
#> 6 07 -105.705479 196 2023.872 http://vertnet.org…
#> 7 07 -105.705479 196 2023.872 http://vertnet.org…
#> 8 07 -105.705479 196 2023.872 http://vertnet.org…
#> 9 07 -105.705479 196 2023.872 http://vertnet.org…
#> 10 07 -105.705479 196 2023.872 http://vertnet.org…
Contributors
- Scott Chamberlain @sckott
- Chris Ray @Pika8tona
- Vijay Barve @vijaybarve
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rvertnet in R doing citation(package = 'rvertnet')
- Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Try the rvertnet package in your browser
Any scripts or data that you put into this service are public.
rvertnet documentation built on May 14, 2021, 1:07 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
rvertnet
rvertnet is a client for interacting with VertNet.org.
VertNet.org API docs: https://github.com/VertNet/webapp/wiki/The-API-search-function
Installation
Stable CRAN version
install.packages("rvertnet")
Or development version from GitHub
remotes::install_github("ropensci/rvertnet")
library('rvertnet')
Search by term
Search for Aves in the state of California, limit to 10 records
res <- searchbyterm(class = "Aves", stateprovince = "California",
limit = 10, messages = FALSE)
Inspect metadata
res$meta
#> $request_date
#> [1] "2021-05-12T23:08:19.676358"
#>
#> $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___9IClAAWgsJqvR3VAbTv8MQA2Cl4NG4AhINRG9jdW1lbnRJbmRleBruAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKE9SIChRVCAiQXZlcyIgInJ0ZXh0X2NsYXNzIikgKElTICJyYXRvbV9jbGFzcyIgImF2ZXMiKSkgKFFUICJDYWxpZm9ybmlhIiAicnRleHRfc3RhdGVwcm92aW5jZSIpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"
#>
#> $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 = "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, 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.
Try the rvertnet package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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