brranching 0.7.0

brranching 0.6.0

the APG dataset in taxize package was updated in taxize v0.9.97 - changes made to comply with the changes in the APG dataset structure (#41)

now using package conditionz in the phylomatic_names() function for handling messages from the taxize package about the user not having an API key set (#36) (#40)

require newest phylocomr version that has fixes for various mis-behavior (#38) (#39)

in the phylomatic_local() function now using phylocomr::ph_phylomatic instead of shelling out to Phylocom via system. A number of parameters are gone due to the change internally (#30) (#35)
in the rbladj() function now using phylocomr::ph_bladj instead of shelling out to Phylocom via system (#30) (#35)
added a package vignette (#31) (#34) thanks @fozy81
added new dataset of four phylogenetic trees that can be used in phylomatic_local(), see ?phylomatic_trees

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)

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)