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Changelog

Source: NEWS.md

treeio 1.30.0

  • Bioconductor RELEASE_3_20 (2024-10-30, Wed)

treeio 1.29.2

treeio 1.29.1

treeio 1.28.0

  • Bioconductor RELEASE_3_19 (2024-05-15, Wed)

treeio 1.27.1

treeio 1.26.0

  • Bioconductor RELEASE_3_18 (2023-10-25, Wed)

treeio 1.25.4

  • reexport as.phylo.hclust_node() to fix as.phylo.pvclust() issue (2023-8-25, Fri, #110)

treeio 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)

treeio 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)

treeio 1.25.1

  • bug fixed in read.nhx() when metadata contains both character and numeric (e.g., AAA111) (2023-05-31, Wed, #97)

treeio 1.24.0

  • Bioconductor RELEASE_3_17 (2023-05-03, Wed)

treeio 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

treeio 1.22.0

  • Bioconductor RELEASE_3_16 (2022-11-02, Wed)

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

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

treeio 1.15.5

treeio 1.15.4

treeio 1.15.3

treeio 1.15.2

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

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,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)

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
  • 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 (2018-08-07, Tue)

treeio 1.5.2

treeio 1.5.1

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

treeio 1.3.13

treeio 1.3.12

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>

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

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

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

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>