rvertnet v0.7.0

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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.

Readme

rvertnet

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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     -121.85760

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, 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 rows

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", 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.
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

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rvertnet in R doing citation(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.

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Functions in rvertnet

Name Description
traitsearch Trait focused search
vertproviders This function is defunct.
rvertnet-defunct Defunct functions in rvertnet
vertavailablemaps This function is defunct.
rvertnet-package Search VertNet archives using R
vertmap Make a simple map to visualize VertNet data.
vertoccurrence This function is defunct.
vertlocations This function is defunct.
vert_id Search by Vertnet occurrence ID
searchbyterm Search by term
vertsearch Find records using a global full-text search of VertNet archives.
vertsummary Summarize a set of records downloaded from VertNet.
spatialsearch Find records within some distance of a point given latitude and longitude.
dump-defunct These functions are defunct
vertoccurrencecount This function is defunct.
verttaxa This function is defunct.
bigsearch Request to download a large number of VertNet records.
No Results!

Vignettes of rvertnet

Name
rvertnet_vignette.Rmd
No Results!

Last month downloads

Details

License MIT + file LICENSE
LazyData true
URL https://github.com/ropensci/rvertnet
BugReports https://github.com/ropensci/rvertnet/issues
VignetteBuilder knitr
RoxygenNote 6.0.1
X-schema.org-applicationCategory Data Access
X-schema.org-keywords species, occurrences, biodiversity, maps, vertnet, mammals, mammalia, specimens
X-schema.org-isPartOf "https://ropensci.org"
NeedsCompilation no
Packaged 2018-04-17 16:49:00 UTC; sckott
Repository CRAN
Date/Publication 2018-04-17 17:25:43 UTC

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