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treebase (version 0.1.0)

get_nex: imports phylogenetic trees from treebase. internal function

Description

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

Value

  • A list object containing all the trees matching the search (of class phylo)