- 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
-
read.mcmctree for PAML MCMCTree result (2021-06-04, Fri)
- Bioconductor 3.13 release
-
read.beast.newick and write.beast.newick for importing and exporting newick text with metadata in BEAST style (2021-03-11, Thu)
- support parsing tree qza file from qiime2 (2020-03-01, Mon)
- support parsing phyloxml (2021-02-04, Thu)
- bug fixed of parsing nhx, now compatible with missing nhx tag (2020-11-19, Thu)
- remove magrittr::
%<>% as it throw error of ‘Error: could not find function “%>%<-”’ (2020-11-19, Thu)
- Bioconductor 3.12 release (2020-10-28, Wed)
-
as_tibble for pvclust (2020-06-22, Mon)
-
as.phylo and as.treedata methods for pvclust object (2020-06-21, Sun)
- Bioconductor 3.11 release
- 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)
- update citation (2020-02-18, Tue)
- phyloxml parser
read.phyloxml (2019-12-05, Thu)
- support jplace version 1 (2019-11-25, Mon)
-
offspring return integer(0) instead of throw error if input .node is a tip (2019-11-21, Thu)
- Bioconductor 3.10 release
- 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)
-
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)
-
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)
- update test according to the change of default RNG in the comming R-3.6 (2019-04-02, Tue)
-
rescale_tree from ggtree (2019-01-11, Fri)
-
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
- compatible with
tibble v=2.0.0 (2018-11-29, Thu)
-
read.jplace compatible with output of TIPars (2018-08-07, Tue)
- bug fixed of
groupOTU.treedata (2018-05-23, Wed)
- 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)
- rename_taxa (2018-04-19, Thu)
- read.astral (2018-04-17, Tue)
- read.iqtree
- read.beast now compatible with taxa label contains ’, " and space (2018-02-27, Wed)
- update according to rOpenSci comments (2018-02-26, Mon)
- 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>
- 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>
- move treedata class, show, get.fields methods to tidytree <2017-12-14, Thu>
- Exporter.Rmd vignette <2017-12-13, Wed>
- 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>
- export groupClade.phylo method <2017-12-11, Mon>
- re-defined groupOTU and groupClade generic using S3 <2017-12-11, Mon>
- 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>
- support tbl_tree object defined in tidytree <2017-12-08, Fri>
- read.codeml output treedata, remove codeml class and clean up code <2017-12-07, Thu>
- 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
- compatible to parse beast output that only contains HPD range <2017-11-01, Wed>
- BioC 3.6 release <2017-11-01, Wed>
- new project site using blogdown <2017-09-28, Thu>
- parse mlc file without dNdS <2017-08-31, Thu>
- better implementation of merge_tree <2017-08-31, Thu>
- 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>
- remove raxml class, now read.raxml output treedata object <2017-02-28, Tue>
- bug fixed of read.beast <2017-02-27, Mon>
- 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>
- as.treedata.ggtree <2016-12-30, Fri>
- as.treedata.phylo4 & as.treedata.phylo4d <2016-12-28, Wed>
- groupOTU, groupClade, gzoom methods from ggtree <2016-12-21, Wed>
- add unit test of NHX (move from ggtree) <2016-12-14, Wed>
- fixed BiocCheck by adding examples <2016-12-07, Wed>
- fixed link in DESCRIPTION <2016-12-06, Tue>
- add vignette <2016-12-06, Tue>
- move parser functions from ggtree <2016-12-06, Tue>
-
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>
