Changes in version 1.7.4 - update test according to the change of default RNG in the comming R-3.6 (2019-04-02, Tue) Changes in version 1.7.3 - rescale_tree from ggtree (2019-01-11, Fri) Changes in version 1.7.2 - MRCA methods for phylo and treedata (2019-01-10, Thu) - mv vignettes to treedata-book - root method from ggtree::reroot (2018-12-28, Fri) - rename to root for importing ape::root generic Changes in version 1.7.1 - compatible with tibble v=2.0.0 (2018-11-29, Thu) Changes in version 1.6.0 - Bioconductor 3.8 release Changes in version 1.5.3 - read.jplace compatible with output of TIPars (2018-08-07, Tue) Changes in version 1.5.2 - bug fixed of as.phylo.ggtree and as.treedata.ggtree (2018-07-19, Thu) - fixed R check for tree_subset by using rlang::quo and import utils::head and utils::tail (2018-05-24, Thu) - tree_subset methods contributed by @tbradley1013 - drop.tip works with tree@extraInfo (2018-05-23, Wed) - https://github.com/GuangchuangYu/tidytree/pull/6#issuecomment-390259901 Changes in version 1.5.1 - bug fixed of groupOTU.treedata (2018-05-23, Wed) - https://github.com/GuangchuangYu/treeio/issues/7 Changes in version 1.4.0 - Bioconductor 3.7 release Changes in version 1.3.15 - Supports convert edge list (matrix, data.frame or tibble) to phylo and treedata object, now ggtree can be used to visualize all tree-like graph. (2018-04-23, Mon) Changes in version 1.3.14 - rename_taxa (2018-04-19, Thu) - https://guangchuangyu.github.io/2018/04/rename-phylogeny-tip-labels-in-treeio/ - read.astral (2018-04-17, Tue) - read.iqtree Changes in version 1.3.13 - mv project website to https://guangchuangyu.github.io/software/treeio - update for rOpenSci acceptance - https://github.com/ropensci/onboarding/issues/179#issuecomment-372127781 Changes in version 1.3.12 - read.beast now compatible with taxa label contains ', " and space (2018-02-27, Wed) - update according to rOpenSci comments (2018-02-26, Mon) - https://github.com/ropensci/onboarding/issues/179#issuecomment-365144565 - https://github.com/ropensci/onboarding/issues/179#issuecomment-366800716 Changes in version 1.3.11 - deprecate read.phyloT as read.tree in ape v5 now supports phyloT newick text <2018-01-11, Thu> - fixed goodpractice check <2018-01-10, Wed> - https://github.com/ropensci/onboarding/issues/179#event-1416196637 - avoid using = for assignment - avoid code line > 80 characters - avoid sapply, instead using vapply and lapply - avoid using 1:length, 1:nrow and 1:ncol, use seq_len and seq_along - more unit tests Changes in version 1.3.10 - added 'Parsing jtree format' session in Importer vignette <2017-12-20, Wed> - added 'Exporting tree data to JSON format' in Exporter vignette - read.jtree and write.jtree functions - added 'Combining tree with external data' and 'Merging tree data from different sources' sessions in Exporter vignette - added 'Combining tree data' and 'Manipulating tree data using tidytree' sessions in Importer vignette - full_join method for treedata object and added 'Linking external data to phylogeny' session in Importer vignette <2017-12-15, Fri> Changes in version 1.3.9 - move treedata class, show, get.fields methods to tidytree <2017-12-14, Thu> - Exporter.Rmd vignette <2017-12-13, Wed> Changes in version 1.3.8 - mv treeio.Rmd vignette to Importer.Rmd and update the contents <2017-12-13, Wed> - write.beast for treedata object <2017-12-12, Tue> - 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 - export groupClade.phylo method <2017-12-11, Mon> Changes in version 1.3.6 - re-defined groupOTU and groupClade generic using S3 <2017-12-11, Mon> Changes in version 1.3.5 - parent, ancestor, child, offspring, rootnode and sibling generic and method for phylo <2017-12-11, Mon> - update mask and merge_tree function according to the treedata object <2017-12-11, Mon> Changes in version 1.3.4 - support tbl_tree object defined in tidytree <2017-12-08, Fri> Changes in version 1.3.3 - read.codeml output treedata, remove codeml class and clean up code <2017-12-07, Thu> Changes in version 1.3.2 - read.codeml_mlc output treedata object and remove codeml_mlc class <2017-12-06, Wed> - read.paml_rst output treedata and remove paml_rst class <2017-12-06, Wed> - read.phylip.tree and read.phylip.seq - read.phylip output treedata object and phylip class definition was removed - read.hyphy output treedata object; hyphy class definition was removed - remove r8s class, read.r8s now output multiPhylo object - jplace class inherits treedata <2017-12-05, Tue> - using treedata object to store beast and mrbayes tree - export read.mrbayes Changes in version 1.3.1 - 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 - BioC 3.6 release <2017-11-01, Wed> Changes in version 1.1.2 - new project site using blogdown <2017-09-28, Thu> Changes in version 1.1.1 - 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 - better implementation of merge_tree <2017-08-31, Thu> Changes in version 0.99.11 - bug fixed in get.fields method for paml_rst <2017-03-20, Mon> - fixed raxml2nwk for using treedata as output of read.raxml <2017-03-17, Fri> - taxa_rename function <2017-03-15, Wed> - phyPML method moved from ggtree <2017-03-06, Mon> Changes in version 0.99.10 - remove raxml class, now read.raxml output treedata object <2017-02-28, Tue> - bug fixed of read.beast <2017-02-27, Mon> Changes in version 0.99.9 - read.newick for parsing node.label as support values <2017-01-03, Tue> - read.beast support MrBayes output <2016-12-30, Fri> - export as.phylo.ggtree <2016-12-30, Fri> Changes in version 0.99.8 - as.treedata.ggtree <2016-12-30, Fri> - as.treedata.phylo4 & as.treedata.phylo4d <2016-12-28, Wed> Changes in version 0.99.7 - groupOTU, groupClade, gzoom methods from ggtree <2016-12-21, Wed> Changes in version 0.99.6 - add unit test of NHX (move from ggtree) <2016-12-14, Wed> Changes in version 0.99.3 - fixed BiocCheck by adding examples <2016-12-07, Wed> Changes in version 0.99.1 - fixed link in DESCRIPTION <2016-12-06, Tue> Changes in version 0.99.0 - add vignette <2016-12-06, Tue> - move parser functions from ggtree <2016-12-06, Tue> Changes in version 0.0.1 - read.nhx from ggtree <2016-12-06, Tue> - as.phylo.treedata to access phylo from treedata object <2016-12-06, Tue> - as.treedata.phylo to convert phylo to tree data object <2016-12-06, Tue> - treedata class definition <2016-12-06, Tue>