@sckott sckott released this Apr 13, 2016 · 70 commits to master since this release

NEW FEATURES

  • Added function phylomatic_local() to use Phylomatic locally.
    Phylomatic is a set of Awk scripts, which have to be downloaded
    by the user. After downloading, this function uses the local version
    of Phylomatic (Same as that that runs as a web service). This is
    advantageous especially when dealing with large queries. (#13)

MINOR IMPROVEMENTS

  • Fixed clean parameter in phylomatic() and phylomatic_local()
    to expect a logical (TRUE or FALSE) instead of a "true" or "false". (#15)
  • A related change to that above, changed reading newick strings to use
    phytools::read.newick() instead of ape::read.tree(), which handles
    the result of clean=FALSE in phylomatic() and phylomatic_local() (#16)
  • Documented that in the storedtree parameter of phylomatic() and
    phylomatic_local() the tree from Zanne et al. is also available by using
    storedtree="zanne2014" (#19)
Assets 2