treebase (version 0.1.5)

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
)

Value

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

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