treebase (version 0.0-6)

get_study: return the trees in treebase that correspond to the search results get_study is deprecated, and now can be performed more easily using phylo_metadata and oai_metadata search functions.

Description

return the trees in treebase that correspond to the search results get_study is deprecated, and now can be performed more easily using phylo_metadata and oai_metadata search functions.

Usage

get_study(search_results, curl = getCurlHandle(), ...)

Arguments

search_results

the output of download_metadata, or a subset thereof

curl

the handle to the curl web utility for repeated calls, see the getCurlHandle() function in RCurl package for details.

...

additional arguments to pass to search_treebase

Value

• all corresponding phylogenies.

Details

this function is commonly used to get trees corresponding to the metadata search.

Examples

all <- download_metadata("", by="all")
nature <- sapply(all, function(x) length(grep("Nature", x$publisher))>0)
science <- sapply(all, function(x) length(grep("^Science$", x$publisher))>0)
s <- treebase:::get_study( all[nature] )
s <- treebase:::get_study(all[science])