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>