Introduction to ridigbio

The ridigbio package can be used to obtain records from iDigBio API’s, including both the Search API and the Media APIs.

General Overview

In this demo we will cover how to:

  1. Install ridigbio
  2. Search for records with idig_search_records()
  3. Search for media records with idig_search_media()

Getting Started

First, you must install the ridigbio package. If you are new to R and R studio, please refer to our QUBES module to get started: Introduction to R with Biodiversity Data, doi:10.25334/84FC-TE88 .

The lastest version of our R package can be installed via CRAN.

install.packages("ridigbio")

Before downloading any records, you must load the ridigbio package.

library(ridigbio)

Download Records

To download records from the Search API, we will use the function idig_search_records(). Here the rq, or record query, indicates we want to download all the records where the scientificname is equal to Galax urceolata.

galax_records <- idig_search_records(rq=list(scientificname="Galax urceolata"))
colnames(galax_records)
##  [1] "uuid"               "occurrenceid"       "catalognumber"     
##  [4] "family"             "genus"              "scientificname"    
##  [7] "country"            "stateprovince"      "geopoint.lon"      
## [10] "geopoint.lat"       "data.dwc:eventDate" "data.dwc:year"     
## [13] "data.dwc:month"     "data.dwc:day"       "collector"         
## [16] "recordset"

When fields are not specified, default columns include the following:

Column Description
uuid Universally Unique IDentifier assigned by iDigBio
occurrenceid identifier for the occurrence, https://rs.tdwg.org/dwc/terms/occurrenceID
catalognumber identifier for the record within the collection, https://rs.tdwg.org/dwc/terms/catalogNumber
family scientific name of the family, https://rs.tdwg.org/dwc/terms/family
genus scientific name of the genus, https://rs.tdwg.org/dwc/terms/genus
scientificname scientific name, https://rs.tdwg.org/dwc/terms/scientificName
country country, https://rs.tdwg.org/dwc/terms/country
stateprovince name of the next smaller administrative region than country, https://rs.tdwg.org/dwc/terms/stateProvince
geopoint.lon equivalent to decimalLongitude, https://rs.tdwg.org/dwc/terms/decimalLongitude
geopoint.lat equivalent to decimalLatitude,https://rs.tdwg.org/dwc/terms/decimalLatitude
datecollected Modified field and could lack biological meaning
data.dwc:eventDate equivalent to eventDate, https://dwc.tdwg.org/list/#dwc_eventDate
data.dwc:year year of collection event, https://dwc.tdwg.org/list/#dwc_year
data.dwc:month month of collection event, https://dwc.tdwg.org/list/#dwc_month
data.dwc:day day of collection event
collector equivalent to recordedBy, https://rs.tdwg.org/dwc/terms/recordedBy
recordset indicates the iDigBio recordset the observation belongs too!

Download Media Records

To download media records from the Media API, we will use the function idig_search_media(). Here the rq, or record query, indicates we want to download all the records where the scientificname is equal to Galax urceolata.

galax_media <- idig_search_media(rq=list(scientificname="Galax urceolata"))
colnames(galax_media)
##  [1] "accessuri"      "datemodified"   "dqs"            "etag"          
##  [5] "flags"          "format"         "hasSpecimen"    "licenselogourl"
##  [9] "mediatype"      "modified"       "recordids"      "records"       
## [13] "recordset"      "rights"         "tag"            "type"          
## [17] "uuid"           "version"        "webstatement"   "xpixels"       
## [21] "ypixels"

When fields are not specified, default columns include the following:

Column Description
accessuri Unique identifier for a resource, https://ac.tdwg.org/termlist/#ac_accessURI
datemodified date last modified, which is assigned by iDigBio
dqs data quality score assigned by iDigBio
etag tag assigned by iDigBio
flags data quality flag assigned by iDigBio
format media format, https://purl.org/dc/terms/format
hasSpecimen TRUE or FALSE, indicates if there is an associated record for this media
licenselogourl media license, https://ac.tdwg.org/termlist/#ac_licenseLogoURL)
mediatype media object type
modified date modified, https://purl.org/dc/terms/modified
recordids list of UUID for associated records
records UUID for the associated record. Use this field to connect Record downloads with Media downloads
recordset indicates the iDigBio recordset the observation belongs too!
rights media rights, https://purl.org/dc/terms/rights
tag general keywords or tags, https://rs.tdwg.org/ac/terms/tag
type media type, https://purl.org/dc/terms/type
uuid Universally Unique IDentifier assigned by iDigBio
version media record version assigned by iDigBio
webstatement media rights, https://developer.adobe.com/xmp/docs/XMPNamespaces/xmpRights/
xpixels as defined by EXIF, x dimension in pixel
ypixels as defined by EXIF,y dimension in pixels

More ways to search

The media search above retained 341 rows, however some of these observations do not have information in the accessuri field. To only obtain records with acessuri, we indicate we only want records where data.ac:accessURI exist, by setting mq, or media query, as followed:

galax_media2 <- idig_search_media(rq=list(scientificname="Galax urceolata"),
                                  mq=list("data.ac:accessURI"=list("type"="exists")))

Now we have 327 observations with accessuri!