DownloadHierarchy: Download Hierarchy Content From Contributors

Description

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.

Usage

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

Arguments

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

Value

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).

Examples

Run this code

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")

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