rvertnet introduction

rvertnet is a client for interacting with VertNet.org.

Installation

You can install the stable version from CRAN:

install.packages("rvertnet")

Or the development version from GitHub using the devtools package:

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", limit = 10, verbose = FALSE)
head(res[,1:5])

##       type                   institutionid institutioncode collectioncode
## 1 specimen http://grbio.org/cool/i64g-wjcr            CUMV Bird specimens
## 2 specimen http://grbio.org/cool/i64g-wjcr            CUMV Bird specimens
## 3 specimen http://grbio.org/cool/i64g-wjcr            CUMV Bird specimens
## 4 specimen http://grbio.org/cool/i64g-wjcr            CUMV Bird specimens
## 5 specimen http://grbio.org/cool/i64g-wjcr            CUMV Bird specimens
## 6 specimen http://grbio.org/cool/i64g-wjcr            CUMV Bird specimens
##       basisofrecord
## 1 PreservedSpecimen
## 2 PreservedSpecimen
## 3 PreservedSpecimen
## 4 PreservedSpecimen
## 5 PreservedSpecimen
## 6 PreservedSpecimen

Search for Mustela nigripes in the states of Wyoming or South Dakota, limit to 20 records

res <- searchbyterm(specificepithet = "nigripes", genus = "Mustela", state = "(wyoming OR south dakota)", limit = 20, verbose=FALSE)
head(res[,1:4])

##       type                   institutionid institutioncode
## 1 specimen http://grbio.org/cool/iakn-125z              KU
## 2 specimen   urn:lsid:biocol.org:col:34495             MSB
## 3 specimen   urn:lsid:biocol.org:col:34925            AMNH
## 4 specimen   urn:lsid:biocol.org:col:35013            DMNS
## 5 specimen   urn:lsid:biocol.org:col:35013            DMNS
## 6 specimen   urn:lsid:biocol.org:col:35013            DMNS
##     collectioncode
## 1              KUM
## 2 Mammal specimens
## 3          Mammals
## 4 Mammal specimens
## 5 Mammal specimens
## 6 Mammal specimens

Search for class Aves, in the state of Nevada, with a coordinate uncertainty range (in meters) of less than 25 meters

res <- searchbyterm(class = "Aves", stateprovince = "Nevada", error = "<25", verbose=FALSE)
head(res[,1:5])

##          type                 institutionid                  collectionid
## 1 observation urn:lsid:biocol.org:col:34777                          <NA>
## 2    specimen urn:lsid:biocol.org:col:34777 urn:lsid:biocol.org:col:34952
##   institutioncode    collectioncode
## 1             MVZ Bird observations
## 2             MVZ    Bird specimens

Email dump of 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

Spatial search service allows only to search on a point defined by latitud and longitude pair, with a radius (meters) from that point. All three parameters are required.

res <- spatialsearch(lat = 33.529, lon = -105.694, radius = 2000, limit = 10, verbose = FALSE)
head(res[,1:5])

##       type                 institutionid                  collectionid
## 1 specimen urn:lsid:biocol.org:col:34495 urn:lsid:biocol.org:col:34950
## 2 specimen urn:lsid:biocol.org:col:34495                          <NA>
## 3 specimen urn:lsid:biocol.org:col:34495                          <NA>
## 4 specimen urn:lsid:biocol.org:col:34495                          <NA>
## 5 specimen urn:lsid:biocol.org:col:34495                          <NA>
## 6 specimen urn:lsid:biocol.org:col:34495                          <NA>
##   institutioncode   collectioncode
## 1             MSB   Bird specimens
## 2             MSB Mammal specimens
## 3             MSB Mammal specimens
## 4             MSB Mammal specimens
## 5             MSB Mammal specimens
## 6             MSB Mammal specimens

Messages

In the previous examples, we've suppressed messages for more concise output, but you can set verbose=TRUE to get helpful messages - verbose=TRUE is also the default setting so if you don't specify that parameter messages will be printed to the console.

res <- searchbyterm(class = "Aves", state = "California", limit = 10, verbose = TRUE)

## Processing request...
## 
## Query/URL: "http://api.vertnet-portal.appspot.com/api/search?q=%7B%22q%22:%22class:Aves%20stateprovince:California%22,%22l%22:10%7D"
## 
## 
## Query date: 2015-01-21T00:41:43.941430
## 
## 
## Matching records: 10 returned, >10000 available