CHANGES IN VERSION 1.3.9 ------------------------ o Exporter.Rmd vignette <2017-12-13, Wed> CHANGES IN VERSION 1.3.8 ------------------------ o mv treeio.Rmd vignette to Importer.Rmd and update the contents <2017-12-13, Wed> o write.beast for treedata object <2017-12-12, Tue> o add "connect" parameter in groupOTU <2017-12-12, Tue> + https://groups.google.com/forum/#!msg/bioc-ggtree/Q4LnwoTf1DM/yEe95OFfCwAJ CHANGES IN VERSION 1.3.7 ------------------------ o export groupClade.phylo method <2017-12-11, Mon> CHANGES IN VERSION 1.3.6 ------------------------ o re-defined groupOTU and groupClade generic using S3 <2017-12-11, Mon> CHANGES IN VERSION 1.3.5 ------------------------ o parent, ancestor, child, offspring, rootnode and sibling generic and method for phylo <2017-12-11, Mon> o update mask and merge_tree function according to the treedata object <2017-12-11, Mon> CHANGES IN VERSION 1.3.4 ------------------------ o support tbl_tree object defined in tidytree <2017-12-08, Fri> CHANGES IN VERSION 1.3.3 ------------------------ o read.codeml output treedata, remove codeml class and clean up code <2017-12-07, Thu> CHANGES IN VERSION 1.3.2 ------------------------ o read.codeml_mlc output treedata object and remove codeml_mlc class <2017-12-06, Wed> o read.paml_rst output treedata and remove paml_rst class <2017-12-06, Wed> o read.phylip.tree and read.phylip.seq o read.phylip output treedata object and phylip class definition was removed o read.hyphy output treedata object; hyphy class definition was removed o remove r8s class, read.r8s now output multiPhylo object o jplace class inherits treedata <2017-12-05, Tue> o using treedata object to store beast and mrbayes tree o export read.mrbayes CHANGES IN VERSION 1.3.1 ------------------------ o compatible to parse beast output that only contains HPD range <2017-11-01, Wed> + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/RF2Ly52U_gc/jEP97nNPAwAJ CHANGES IN VERSION 1.2.0 ------------------------ o BioC 3.6 release <2017-11-01, Wed> CHANGES IN VERSION 1.1.2 ------------------------ o new project site using blogdown <2017-09-28, Thu> CHANGES IN VERSION 1.1.1 ------------------------ o parse mlc file without dNdS <2017-08-31, Thu> + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/hTRj-uldgAg o better implementation of merge_tree <2017-08-31, Thu> CHANGES IN VERSION 0.99.11 ------------------------ o bug fixed in get.fields method for paml_rst <2017-03-20, Mon> o fixed raxml2nwk for using treedata as output of read.raxml <2017-03-17, Fri> o taxa_rename function <2017-03-15, Wed> o phyPML method moved from ggtree <2017-03-06, Mon> CHANGES IN VERSION 0.99.10 ------------------------ o remove raxml class, now read.raxml output treedata object <2017-02-28, Tue> o bug fixed of read.beast <2017-02-27, Mon> CHANGES IN VERSION 0.99.9 ------------------------ o read.newick for parsing node.label as support values <2017-01-03, Tue> o read.beast support MrBayes output <2016-12-30, Fri> o export as.phylo.ggtree <2016-12-30, Fri> CHANGES IN VERSION 0.99.8 ------------------------ o as.treedata.ggtree <2016-12-30, Fri> o as.treedata.phylo4 & as.treedata.phylo4d <2016-12-28, Wed> CHANGES IN VERSION 0.99.7 ------------------------ o groupOTU, groupClade, gzoom methods from ggtree <2016-12-21, Wed> CHANGES IN VERSION 0.99.6 ------------------------ o add unit test of NHX (move from ggtree) <2016-12-14, Wed> CHANGES IN VERSION 0.99.3 ------------------------ o fixed BiocCheck by adding examples <2016-12-07, Wed> CHANGES IN VERSION 0.99.1 ------------------------ o fixed link in DESCRIPTION <2016-12-06, Tue> CHANGES IN VERSION 0.99.0 ------------------------ o add vignette <2016-12-06, Tue> o move parser functions from ggtree <2016-12-06, Tue> CHANGES IN VERSION 0.0.1 ------------------------ o read.nhx from ggtree <2016-12-06, Tue> o as.phylo.treedata to access phylo from treedata object <2016-12-06, Tue> o as.treedata.phylo to convert phylo to tree data object <2016-12-06, Tue> o treedata class definition <2016-12-06, Tue>