DownloadHierarchy: Download Hierarchy Content From Contributors
In Reol: R interface to the Encyclopedia of Life

Description Usage Arguments Value See Also Examples

This function will use the EOL pages to find the provider information (ie which providers contribute information to the pages). Hierarchies get downloaded as hier pages rather than eol pages. Providers contribute information on taxonomic rankings, hierarchical tree structure, synonyms, etc. Some providers only contribute certain kinds of information; for example not all will provide synonyms or taxonomic hierarchy information.

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ProviderCount(MyEOLs,verbose=FALSE)
BestProvider(MyEOLs)
DownloadHierarchy(MyEOLs, to.file=TRUE, database=NULL, verbose=TRUE, ...)

`MyEOLs`	A vector of filenames for downloaded EOL pages
`to.file`	Whether to download data to a file
`database`	Provider hierarchy information to use
`verbose`	An optional print statement during download
`...`	further arguments to be passed to `DownloadHierarchy`

ProviderCount will give a named vector back of all of the providers that contribute to the set of MyEOLs taxa, and the number of taxa they contribute. The maximum number of species a provider can contribute will be the number of taxa in MyEOLs. Usually, ITIS, GBIF, and NCBI are top contributors (but this varies depending on scale). BestProvider will choose the top provider from this list (even if there are ties). DownloadHierarchy will download the XML information either to a file (to.file=TRUE) or as a single R object as a list (to.file=FALSE).

DownloadEOLpages DownloadSearchedTaxa

data(MyEOLs)
## Not run: ProviderCount(MyEOLs[6], verbose=TRUE)
BestProvider(MyEOLs[6])
## End(Not run)
DownloadHierarchy(MyEOLs[6], FALSE, database="NCBI Taxonomy")
	
#Download data from whichever provider has the most coverage
## Not run: MyHiers <- DownloadHierarchy(MyEOLs, to.file=TRUE, BestProvider(MyEOLs))
	
#Or download from a specific provider
## Not run: MyHiers <- DownloadHierarchy(MyEOLs, FALSE, database="NCBI Taxonomy")