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>