# treeio 1.21.3 + update `as.phylo` and `as.treedata` for data.frame object (2022-10-31, Mon, #88) + `as.phylo()` method for `list` (2022-09-14, Wed, #86) # treeio 1.21.2 + update `as.treedata.pvclust` method (2022-08-15, Mon, #82) + add citation of the tree data book (2022-08-13, Sat) # treeio 1.21.1 + `read.nextstrain.json()` function to parse json tree file from NextStrain (2022-08-03, Wed, #81) # treeio 1.20.0 + Bioconductor 3.15 relase # treeio 1.19.2 + update `offspring()` to work as `child()`. Actually they are using the same function with different default (`child(type = "children")` and `offspring(type="all")`) (2022-03-16, Wed) + update `child()` to support different types ("children", 'tips', 'internal', 'external', 'all') (2022-03-09, Wed, #75) + `write.beast` allows `treedata` object only contains `phylo` slot, then it will equivalent to `write.nexus` (2022-02-23, Wed) # treeio 1.19.1 + bug fixed in `groupClade.treedata` to return a `treedata` object instead of `phylo` (2021-11-12, Fri) # treeio 1.18.0 + Bioconductor 3.14 release # treeio 1.17.2 + allow additional parameter to pass to `drop.tip` methods (2021-06-23, Wed, @xiangpin, #62) + `as.phylo` and `as.treedata` for `data.frame` (2021-06-12, Sat) + `as.ultrametric` method to force a tree to be ultrametric (2021-06-09, Wed) + introduce `force.ultrametric` parameter in `read.mcmctree` # treeio 1.17.1 + `read.mcmctree` for PAML MCMCTree result (2021-06-04, Fri) # treeio 1.16.0 + Bioconductor 3.13 release # treeio 1.15.6 + optimized `read.nhx` for large tree file (2021-03-12, Fri) - # treeio 1.15.5 + `read.beast.newick` and `write.beast.newick` for importing and exporting newick text with metadata in BEAST style (2021-03-11, Thu) - # treeio 1.15.4 + support parsing tree qza file from qiime2 (2020-03-01, Mon) - # treeio 1.15.3 + support parsing phyloxml (2021-02-04, Thu) - # treeio 1.15.2 + bug fixed of parsing nhx, now compatible with missing nhx tag (2020-11-19, Thu) - # treeio 1.15.1 + remove magrittr::`%<>%` as it throw error of 'Error: could not find function "%>%<-"' (2020-11-19, Thu) # treeio 1.14.0 + Bioconductor 3.12 release (2020-10-28, Wed) # treeio 1.13.1 + `as_tibble` for `pvclust` (2020-06-22, Mon) + `as.phylo` and `as.treedata` methods for `pvclust` object (2020-06-21, Sun) # treeio 1.12.0 + Bioconductor 3.11 release # treeio 1.11.3 + change according to dplyr (v=1.0.0) (2020-04-09, Thu) - remove mutate_, rename_, select_ and group_by_ + remove data_frame for it was deprecated in tibble (v=3.0.0) # treeio 1.11.2 + update citation (2020-02-18, Tue) + phyloxml parser `read.phyloxml` (2019-12-05, Thu) # treeio 1.11.1 + support jplace version 1 (2019-11-25, Mon) - + `offspring` return `integer(0)` instead of throw error if input `.node` is a tip (2019-11-21, Thu) # treeio 1.10.0 + Bioconductor 3.10 release # treeio 1.9.3 + add citation information (2019-10-05, Sta) + rename `phyPML` to `as.treedata.pml` (2019-10-01, Tue) + `as.phylo` method for `igraph` (only work with tree graph) (2019-09-28, Sat) # treeio 1.9.2 + `nodeid` and `nodelab` methods for converting between node number and labels (2019-08-09, Fri) + `parent`, 'ancestor`, `child`, `offspring` and `rootnode` methods for `treedata` (2019-08-07, Wed) + `read.mega_tabular` to parse MEGA Tabular output (2019-07-16, Tue) + `read.mega` to parse MEGA NEXUS (actually BEAST compatible) # treeio 1.9.1 + `rename_taxa` now use 1st column as key and 2nd column as value by default (2019-05-28, Tue) + enable `tree_subset` to specify `group_name` and enable to incorporate `root.edge` by setting `root_edge = TRUE` (2019-05-27, Mon) + `full_join` method for phylo object (2019-05-22, Wed) + redefined root method to wrape `ape::root.phylo` for compatibility (2019-05-20, Mon) - # treeio 1.8.0 + Bioconductor 3.9 release # treeio 1.7.4 + update test according to the change of default RNG in the comming R-3.6 (2019-04-02, Tue) # treeio 1.7.3 + `rescale_tree` from `ggtree` (2019-01-11, Fri) # treeio 1.7.2 + `MRCA` methods for `phylo` and `treedata` (2019-01-10, Thu) + mv vignettes to [treedata-book](https://yulab-smu.github.io/treedata-book/) + `root` method from `ggtree::reroot` (2018-12-28, Fri) - rename to `root` for importing `ape::root` generic # treeio 1.7.1 + compatible with `tibble` v=2.0.0 (2018-11-29, Thu) # treeio 1.6.0 + Bioconductor 3.8 release # treeio 1.5.3 + `read.jplace` compatible with output of [TIPars](https://github.com/id-bioinfo/TIPars) (2018-08-07, Tue) # treeio 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](https://github.com/tbradley1013) + `drop.tip` works with `tree@extraInfo` (2018-05-23, Wed) - # treeio 1.5.1 + bug fixed of `groupOTU.treedata` (2018-05-23, Wed) - # treeio 1.4.0 + Bioconductor 3.7 release # treeio 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) # treeio 1.3.14 + rename_taxa (2018-04-19, Thu) - + read.astral (2018-04-17, Tue) + read.iqtree # treeio 1.3.13 + mv project website to + update for rOpenSci acceptance - # treeio 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) - - # treeio 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> - - 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 # treeio 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> # treeio 1.3.9 * move treedata class, show, get.fields methods to tidytree <2017-12-14, Thu> * Exporter.Rmd vignette <2017-12-13, Wed> # treeio 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> + # treeio 1.3.7 * export groupClade.phylo method <2017-12-11, Mon> # treeio 1.3.6 * re-defined groupOTU and groupClade generic using S3 <2017-12-11, Mon> # treeio 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> # treeio 1.3.4 * support tbl_tree object defined in tidytree <2017-12-08, Fri> # treeio 1.3.3 * read.codeml output treedata, remove codeml class and clean up code <2017-12-07, Thu> # treeio 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 # treeio 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 # treeio 1.2.0 * BioC 3.6 release <2017-11-01, Wed> # treeio 1.1.2 * new project site using blogdown <2017-09-28, Thu> # treeio 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> # treeio 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> # treeio 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> # treeio 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> # treeio 0.99.8 * as.treedata.ggtree <2016-12-30, Fri> * as.treedata.phylo4 & as.treedata.phylo4d <2016-12-28, Wed> # treeio 0.99.7 * groupOTU, groupClade, gzoom methods from ggtree <2016-12-21, Wed> # treeio 0.99.6 * add unit test of NHX (move from ggtree) <2016-12-14, Wed> # treeio 0.99.3 * fixed BiocCheck by adding examples <2016-12-07, Wed> # treeio 0.99.1 * fixed link in DESCRIPTION <2016-12-06, Tue> # treeio 0.99.0 * add vignette <2016-12-06, Tue> * move parser functions from ggtree <2016-12-06, Tue> # treeio 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 `treedata` object <2016-12-06, Tue> * `treedata` class definition <2016-12-06, Tue>