imports phylogenetic trees from treebase. internal function
Usage
get_nex(query, max_trees = "last()", returns = "tree",
curl = getCurlHandle(), verbose = TRUE, pause1 = 1, pause2 = 1,
attempts = 5, only_metadata = FALSE)Arguments
- query
: a phylows formatted search, see https://sourceforge.net/apps/mediawiki/treebase/index.php?title=API
- max_trees
limits the number of trees returned should be kept.
- returns
should return the tree object or the matrix (of sequences)
- curl
the handle to the curl
- verbose
a logical indicating if output should be printed to screen
- pause1
number of seconds to hesitate between requests
- pause2
number of seconds to hesitate between individual files
- attempts
number of attempts to access a particular resource