Changes in version 1.29.2 - speedup read.beast() with multithreading supports (2024-10-27, Sun, #128) Changes in version 1.29.1 - use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri) - support treetime output (2024-07-18, Thu) - https://treetime.readthedocs.io/en/latest/tutorials/clock.html Changes in version 1.28.0 - Bioconductor RELEASE_3_19 (2024-05-15, Wed) Changes in version 1.27.1 - added support for multiple trees / writing phylo objects in write.beast() (2024-04-08, Mon, #113) - speed up read.beast() (2023-12-13, Wed, #118) - optimize write.jtree() (2023-12-13, Wed, #117) - write.jplace() method to export jplace object to a jplace file (2023-11-27, Mon, #112, #115) Changes in version 1.26.0 - Bioconductor RELEASE_3_18 (2023-10-25, Wed) Changes in version 1.25.4 - reexport as.phylo.hclust_node() to fix as.phylo.pvclust() issue (2023-8-25, Fri, #110) Changes in version 1.25.3 - add find.hclust.igraph() method to hierarchical clustering graph nodes (2023-08-11, Fri, #105) - update spt() and as.phylo.igraph() to consider edge attributes (#105) - move tree operation methods to the 'tidytree' package so that this package is focus on input, output and object conversion - fixed issue in parse BEAST file that contains negative branch length (2023-08-03, Thu, #106) Changes in version 1.25.2 - spt method to find shortest path tree (2023-07-14, Fri, #102) - update old-style 'CITATION' from citEntry() to bibentry() (2023-07-14, Fri, #102) - bug fixed in as.treedata() for tbl_df object (2023-07-14, Fri, #101) - keep.tip() method to remove all tips excepts the selected tips (2023-07-13, Thu, #100) - better support of converting 'igraph' object to 'phylo' object (2023-07-12, Wed, #99) Changes in version 1.25.1 - bug fixed in read.nhx() when metadata contains both character and numeric (e.g., AAA111) (2023-05-31, Wed, #97) Changes in version 1.24.0 - Bioconductor RELEASE_3_17 (2023-05-03, Wed) Changes in version 1.23.1 - supports converting dendro object (output of ggdendro::dendro_data()) to a phylo object (2023-03-02, Thu, #95) - add inner_join() method to allows appending data of a variable - use nested data structure and tidyr::unnest can extract and convert the data to a simple tibble data frame (#93) - update full_join method (#92) - support standard dplyr UI of by = c( 'columnX' = 'cloumnY') - drop data from external data.frame that are not presented in the tree - use nested column if duplicated rows exist Changes in version 1.22.0 - Bioconductor RELEASE_3_16 (2022-11-02, Wed) Changes in version 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) Changes in version 1.21.2 - update as.treedata.pvclust method (2022-08-15, Mon, #82) - add citation of the tree data book (2022-08-13, Sat) Changes in version 1.21.1 - read.nextstrain.json() function to parse json tree file from NextStrain (2022-08-03, Wed, #81) Changes in version 1.20.0 - Bioconductor 3.15 relase Changes in version 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) Changes in version 1.19.1 - bug fixed in groupClade.treedata to return a treedata object instead of phylo (2021-11-12, Fri) Changes in version 1.18.0 - Bioconductor 3.14 release Changes in version 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 Changes in version 1.17.1 - read.mcmctree for PAML MCMCTree result (2021-06-04, Fri) Changes in version 1.16.0 - Bioconductor 3.13 release Changes in version 1.15.6 - optimized read.nhx for large tree file (2021-03-12, Fri) - https://github.com/YuLab-SMU/treeio/pull/51 Changes in version 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) - https://github.com/YuLab-SMU/treeio/pull/50 Changes in version 1.15.4 - support parsing tree qza file from qiime2 (2020-03-01, Mon) - https://github.com/YuLab-SMU/treeio/pull/46/files Changes in version 1.15.3 - support parsing phyloxml (2021-02-04, Thu) - https://github.com/YuLab-SMU/treeio/pull/44 Changes in version 1.15.2 - bug fixed of parsing nhx, now compatible with missing nhx tag (2020-11-19, Thu) - https://github.com/YuLab-SMU/treeio/pull/40 Changes in version 1.15.1 - remove magrittr::%<>% as it throw error of 'Error: could not find function "%>%<-"' (2020-11-19, Thu) Changes in version 1.14.0 - Bioconductor 3.12 release (2020-10-28, Wed) Changes in version 1.13.1 - as_tibble for pvclust (2020-06-22, Mon) - as.phylo and as.treedata methods for pvclust object (2020-06-21, Sun) Changes in version 1.12.0 - Bioconductor 3.11 release Changes in version 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) Changes in version 1.11.2 - update citation (2020-02-18, Tue) - phyloxml parser read.phyloxml (2019-12-05, Thu) Changes in version 1.11.1 - support jplace version 1 (2019-11-25, Mon) - https://github.com/YuLab-SMU/treeio/pull/25 - offspring return integer(0) instead of throw error if input .node is a tip (2019-11-21, Thu) Changes in version 1.10.0 - Bioconductor 3.10 release Changes in version 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) Changes in version 1.9.2 - nodeid and nodelab methods for converting between node number and labels (2019-08-09, Fri) - parent, 'ancestor, child, offspringandrootnodemethods fortreedata` (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) Changes in version 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) - https://github.com/GuangchuangYu/treeio/issues/18 Changes in version 1.8.0 - Bioconductor 3.9 release 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 treedata object <2016-12-06, Tue> - treedata class definition <2016-12-06, Tue>