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