rvertnet v0.8.0

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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

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] "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 = "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, 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

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

Vignettes of rvertnet

Name
rvertnet.Rmd
No Results!

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Details

License MIT + file LICENSE
LazyData true
URL https://github.com/ropensci/rvertnet (devel) https://docs.ropensci.org/rvertnet (documentation)
BugReports https://github.com/ropensci/rvertnet/issues
VignetteBuilder knitr
Encoding UTF-8
RoxygenNote 7.0.2
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 2020-01-29 17:31:41 UTC; sckott
Repository CRAN
Date/Publication 2020-01-29 17:50:03 UTC

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