NEWS.md

In YuLab-SMU/treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

treeio 1.30.0

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

treeio 1.29.2

• speedup read.beast() with multithreading supports (2024-10-27, Sun, #128)

treeio 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

treeio 1.28.0

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

treeio 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)

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

• 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)
• https://github.com/YuLab-SMU/treeio/pull/51

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)
• https://github.com/YuLab-SMU/treeio/pull/50

treeio 1.15.4

• support parsing tree qza file from qiime2 (2020-03-01, Mon)
• https://github.com/YuLab-SMU/treeio/pull/46/files

treeio 1.15.3

• support parsing phyloxml (2021-02-04, Thu)
• https://github.com/YuLab-SMU/treeio/pull/44

treeio 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

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)
• 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)

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)
• https://github.com/GuangchuangYu/treeio/issues/18

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

• 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

treeio 1.5.1

• bug fixed of groupOTU.treedata (2018-05-23, Wed)
• https://github.com/GuangchuangYu/treeio/issues/7

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)
• https://guangchuangyu.github.io/2018/04/rename-phylogeny-tip-labels-in-treeio/
• read.astral (2018-04-17, Tue)
• read.iqtree

treeio 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

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)
• https://github.com/ropensci/onboarding/issues/179#issuecomment-365144565
• https://github.com/ropensci/onboarding/issues/179#issuecomment-366800716

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>
  • 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

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>
• https://groups.google.com/forum/#!msg/bioc-ggtree/Q4LnwoTf1DM/yEe95OFfCwAJ

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>

YuLab-SMU/treeio documentation built on Nov. 3, 2024, 4:17 p.m.