NEWS.md

In brranching: Fetch 'Phylogenies' from Many Sources

brranching 0.7.0

MINOR IMPROVEMENTS

• vignettes fix (#45)

brranching 0.6.0

MINOR IMPROVEMENTS

• 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)

brranching 0.5.0

MINOR IMPROVEMENTS

• 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)

BUG FIXES

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

brranching 0.4.0

NEW FEATURES

• 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

MINOR IMPROVEMENTS

• added docs to phylomatic_names() and the README on using NCBI Entrez API keys

brranching 0.3.0

NEW FEATURES

• gains new function bladj (#18)
• replaced httr with crul for http requests (#25)

MINOR IMPROVEMENTS

• fix links to readme images (#29) (#26)
• verbose param in phylomatic() function changed to mssgs

brranching 0.2.0

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)

brranching 0.1.0

NEW FEATURES

• Released to CRAN.

brranching documentation built on May 11, 2021, 9:09 a.m.