SymbiotaR2: Downloading data from Symbiota2 portals into R

In pearselab/SymbiotaR2: Downloading Data from Symbiota2 Portals into R

Description

This package allows users to access and download from Symbiota2, a content management system for biodiveristy data.

About

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.

Code Structure

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).

Portal Specification

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

References

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.

Examples

## 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)

pearselab/SymbiotaR2 documentation built on Jan. 30, 2022, 5:11 a.m.