Title: | Downloading Data from Symbiota2 Portals into R |
---|---|
Description: | Download data from Symbiota2 portals using Symbiota's API. Covers the Checklists, Collections, Crowdsource, Exsiccati, Glossary, ImageProcessor, Key, Media, Occurrence, Reference, Taxa, Traits, and UserRoles API families. Each Symbiota2 portal owner can load their own plugins (and modified code), and so this package may not cover every possible API endpoint from a given Symbiota2 instance. |
Authors: | Austin Koontz [aut, cre] |
Maintainer: | Austin Koontz <[email protected]> |
License: | MIT + file LICENSE |
Version: | 0.0-1 |
Built: | 2024-08-29 23:15:31 UTC |
Source: | https://github.com/ropensci/SymbiotaR2 |
Functions that retrieve Checklist resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
ChecklistProjects(id, page, url = NULL) Coordinates(id, page, url = NULL) TaxaLink(id, page, url = NULL) Checklists(id, page, url = NULL)
ChecklistProjects(id, page, url = NULL) Coordinates(id, page, url = NULL) TaxaLink(id, page, url = NULL) Checklists(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a Coordinates resource (id = 1), from a (nonexistent) dummy portal object <- Coordinates(id = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a Coordinates resource (id = 1), from a (nonexistent) dummy portal object <- Coordinates(id = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Collection resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Categories(id, page, url = NULL) Institutions(id, page, url = NULL) Stats(id, page, url = NULL) Collections(id, page, url = NULL)
Categories(id, page, url = NULL) Institutions(id, page, url = NULL) Stats(id, page, url = NULL) Collections(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling in a page of Institutions, from a (nonexistent) dummy portal ints <- Institutions(page = 3, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling in a page of Institutions, from a (nonexistent) dummy portal ints <- Institutions(page = 3, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Crowdsource resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Central(id, page, url = NULL) Queue(id, page, url = NULL)
Central(id, page, url = NULL) Queue(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Acquiring a Queue resource (id = 2), from a (nonexistent) dummy portal object <- Queue(id = 2, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Acquiring a Queue resource (id = 2), from a (nonexistent) dummy portal object <- Queue(id = 2, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Exsiccati resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Numbers(id, page, url = NULL) Titles(id, page, url = NULL)
Numbers(id, page, url = NULL) Titles(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Acquiring a Titles resource (id = 3), from a (nonexistent) dummy portal object <- Titles(id = 3, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Acquiring a Titles resource (id = 3), from a (nonexistent) dummy portal object <- Titles(id = 3, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Glossary resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Glossary(id, page, url = NULL) TermLink(id, page, url = NULL)
Glossary(id, page, url = NULL) TermLink(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Acquiring a page of Glossary resources, from a (nonexistent) dummy portal glossPage <- Glossary(page = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Acquiring a page of Glossary resources, from a (nonexistent) dummy portal glossPage <- Glossary(page = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve ImageProcessor resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Projects(id, page, url = NULL) RawLabels(id, page, url = NULL)
Projects(id, page, url = NULL) RawLabels(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Acquiring a RawLabels resource (id = 1), from a (nonexistent) dummy portal object <- RawLabels(id = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Acquiring a RawLabels resource (id = 1), from a (nonexistent) dummy portal object <- RawLabels(id = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Key resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
CharacterHeading(id, page, url = NULL) Characters(id, page, url = NULL) CharacterStateImages(id, page, url = NULL) CharacterStates(id, page, url = NULL) DescriptionDeletions(id, page, url = NULL)
CharacterHeading(id, page, url = NULL) Characters(id, page, url = NULL) CharacterStateImages(id, page, url = NULL) CharacterStates(id, page, url = NULL) DescriptionDeletions(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a Characters resource (id = 3), from a (nonexistent) dummy portal object <- Characters(id = 3, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a Characters resource (id = 3), from a (nonexistent) dummy portal object <- Characters(id = 3, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Media resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
TagKey(id, page, url = NULL)
TagKey(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a page of TagKey resources, from a (nonexistent) dummy portal object <- TagKey(page = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a page of TagKey resources, from a (nonexistent) dummy portal object <- TagKey(page = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Miscellaneous resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Configurations(id, page, url = NULL) LookupLanguages(id, page, url = NULL) SchemaVersion(id, page, url = NULL)
Configurations(id, page, url = NULL) LookupLanguages(id, page, url = NULL) SchemaVersion(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a Configurations resource (id = 4), from a (nonexistent) dummy portal object <- Configurations(id = 4, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a Configurations resource (id = 4), from a (nonexistent) dummy portal object <- Configurations(id = 4, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Occurrence resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
AccessStats(id, page, url = NULL) Determinations(id, page, url = NULL) Duplicates(id, page, url = NULL) EditLocks(id, page, url = NULL) Edits(id, page, url = NULL) FullText(id, page, url = NULL) GuidDeterminations(id, page, url = NULL) GuidOccurrences(id, page, url = NULL) LookupChronostratigraphy(id, page, url = NULL) LookupCounties(id, page, url = NULL) LookupCountries(id, page, url = NULL) LookupStateProvinces(id, page, url = NULL) UploadMappings(id, page, url = NULL) UploadParameters(id, page, url = NULL) Verification(id, page, url = NULL) Associations(id, page, url = NULL) Comments(id, page, url = NULL) DatasetLink(id, page, url = NULL) Datasets(id, page, url = NULL) Exchange(id, page, url = NULL) Loans(id, page, url = NULL) Occurrences(id, page, url = NULL)
AccessStats(id, page, url = NULL) Determinations(id, page, url = NULL) Duplicates(id, page, url = NULL) EditLocks(id, page, url = NULL) Edits(id, page, url = NULL) FullText(id, page, url = NULL) GuidDeterminations(id, page, url = NULL) GuidOccurrences(id, page, url = NULL) LookupChronostratigraphy(id, page, url = NULL) LookupCounties(id, page, url = NULL) LookupCountries(id, page, url = NULL) LookupStateProvinces(id, page, url = NULL) UploadMappings(id, page, url = NULL) UploadParameters(id, page, url = NULL) Verification(id, page, url = NULL) Associations(id, page, url = NULL) Comments(id, page, url = NULL) DatasetLink(id, page, url = NULL) Datasets(id, page, url = NULL) Exchange(id, page, url = NULL) Loans(id, page, url = NULL) Occurrences(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a page of Occurrences, from a (nonexistent) dummy portal entries <- Occurrence(page = 6, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a page of Occurrences, from a (nonexistent) dummy portal entries <- Occurrence(page = 6, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Reference resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
LookupReferenceTypes(id, page, url = NULL)
LookupReferenceTypes(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a LookupReferenceType resource (id = 1), from a (nonexistent) dummy portal object <- LookupReferenceType(id = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a LookupReferenceType resource (id = 1), from a (nonexistent) dummy portal object <- LookupReferenceType(id = 1, url = "http://dummy-portal.com/api/") ## End(Not run)
This package allows users to access and download from Symbiota2, a content management system for biodiveristy data.
Symbiota2 is the improved, refactored version of Symbiota, an open source content management system for biological specimen data. SymbiotaR2 allows users to access the data available at Symbiota2 portals. By specifying the URL of the relevant portal, and the resource to be downloaded, users can use SymbiotaR2 to deliver biological specimen-data in an R format.
Package functions are organized by API family, which generally group the functions by the type of resource they pull from the portal. Each function can either return an individual resources (through specifying the 'id' argument) or a collection of resources (through specifying the 'page' argument). After providing either the 'id' or the 'page' of resources, and the URL of the relevant portal, SymbiotaR2 will return an R object (for 'id', usually a list; for 'page', usually a data.frame).
All SymbiotaR2 commands require a URL that directs to the Symiobta2 portal to download data from. Users need to make sure they are granted access to a Symbiota2 portal before trying to download data from it.
The address of a Symbiota2 portal is provided as the 'url' string argument to each function. To specify a default URL, use the 'SymbiotaR2_setup' function, which will the default url to your .Rprofile.
This package only allows users to access data from existing Symbiota2 portals; to create a new Symbiota2 portal, see the documentation at https://symbiota2.github.io/Symbiota2/setup/installation.html
https://symbiota.org/docs/
Gries, C., Gilbert, E. E., & Franz, N. M. (2014). Symbiota - A virtual platform for creating voucher-based biodiversity information communities. Biodiversity Data Journal, 2, e1114.
## Not run: myURL <- "http://ImaginarySymbiota2Portal.com/api" myTaxa <- Taxa(id = 12, url = myURL) str(myTaxa) myOccurrences <- Occurrence(page = 2, url = myURL) length(myOccurrences) ## End(Not run)
## Not run: myURL <- "http://ImaginarySymbiota2Portal.com/api" myTaxa <- Taxa(id = 12, url = myURL) str(myTaxa) myOccurrences <- Occurrence(page = 2, url = myURL) length(myOccurrences) ## End(Not run)
Sets the SymbiotaR2_url
option for you, optionally, by
appending it to your .Rprofile
. Checks whether you've
specified a valid URL that can be reached, and attempts to pull
a resource from the API, to confirm that the URL does specify
a Symbiota2 portal.
SymbiotaR2_setup(url, append = FALSE, verbose = TRUE)
SymbiotaR2_setup(url, append = FALSE, verbose = TRUE)
url |
URL of Symbiota2 portal (a trailing |
append |
|
verbose |
|
Invisbly, the URL that has been stored
Will Pearse
## Not run: # An example (that doesn't work because it's not a real portal) SymbiotaR2_setup("http://nonexistent-portal.com/api/") # Trying to save a non-existence portal SymbiotaR2_setup("http://nonexistent-portal.com/api/", TRUE) ## End(Not run)
## Not run: # An example (that doesn't work because it's not a real portal) SymbiotaR2_setup("http://nonexistent-portal.com/api/") # Trying to save a non-existence portal SymbiotaR2_setup("http://nonexistent-portal.com/api/", TRUE) ## End(Not run)
Functions that retrieve Taxa resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Taxa(id, page, url = NULL) Authorities(id, page, url = NULL) DescriptionBlock(id, page, url = NULL) Synonymy(id, page, url = NULL)
Taxa(id, page, url = NULL) Authorities(id, page, url = NULL) DescriptionBlock(id, page, url = NULL) Synonymy(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a page of Taxa resources, from a (nonexistent) dummy portal object <- Taxa(page = 2, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a page of Taxa resources, from a (nonexistent) dummy portal object <- Taxa(page = 2, url = "http://dummy-portal.com/api/") ## End(Not run)
Functions that retrieve Traits resources from the server previously connected to. Each function either retrieves an individual resource or a page of resources, depending on the arguments provided.
Traits(id, page, url = NULL)
Traits(id, page, url = NULL)
id |
id value (usually |
page |
|
url |
URL string of the Symbiota2 portal to be connected to.
A trailing |
If using id
, the specific resource specified;
if using page, the page
specified of resources
To specify a default URL to refer to, see SymbiotaR2_setup()
Austin Koontz
## Not run: # Pulling a Traits resource (id = 4), from a (nonexistent) dummy portal object <- Traits(id = 4, url = "http://dummy-portal.com/api/") ## End(Not run)
## Not run: # Pulling a Traits resource (id = 4), from a (nonexistent) dummy portal object <- Traits(id = 4, url = "http://dummy-portal.com/api/") ## End(Not run)