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)

#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)
- #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)
- #44

treeio 1.15.2

bug fixed of parsing nhx, now compatible with missing nhx tag (2020-11-19, Thu)
- #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)
- #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)
- #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)
- YuLab-SMU/tidytree#6 (comment)

treeio 1.5.1

bug fixed of groupOTU.treedata (2018-05-23, Wed)
- #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
- ropensci/software-review#179 (comment)

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)
- ropensci/software-review#179 (comment)
- ropensci/software-review#179 (comment)

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>
- ropensci/software-review#179 (comment)
- 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>

Files

NEWS.md

Latest commit

History

NEWS.md

File metadata and controls

treeio 1.30.0

treeio 1.29.2

treeio 1.29.1

treeio 1.28.0

treeio 1.27.1

treeio 1.26.0

treeio 1.25.4

treeio 1.25.3

treeio 1.25.2

treeio 1.25.1

treeio 1.24.0

treeio 1.23.1

treeio 1.22.0

treeio 1.21.3

treeio 1.21.2

treeio 1.21.1

treeio 1.20.0

treeio 1.19.2

treeio 1.19.1

treeio 1.18.0

treeio 1.17.2

treeio 1.17.1

treeio 1.16.0

treeio 1.15.6

treeio 1.15.5

treeio 1.15.4

treeio 1.15.3

treeio 1.15.2

treeio 1.15.1

treeio 1.14.0

treeio 1.13.1

treeio 1.12.0

treeio 1.11.3

treeio 1.11.2

treeio 1.11.1

treeio 1.10.0

treeio 1.9.3

treeio 1.9.2

treeio 1.9.1

treeio 1.8.0

treeio 1.7.4

treeio 1.7.3

treeio 1.7.2

treeio 1.7.1

treeio 1.6.0

treeio 1.5.3

treeio 1.5.2

treeio 1.5.1

treeio 1.4.0

treeio 1.3.15

treeio 1.3.14

treeio 1.3.13

treeio 1.3.12

treeio 1.3.11

treeio 1.3.10

treeio 1.3.9

treeio 1.3.8

treeio 1.3.7

treeio 1.3.6

treeio 1.3.5

treeio 1.3.4

treeio 1.3.3

treeio 1.3.2

treeio 1.3.1

treeio 1.2.0

treeio 1.1.2

treeio 1.1.1

treeio 0.99.11

treeio 0.99.10

treeio 0.99.9

treeio 0.99.8

treeio 0.99.7

treeio 0.99.6

treeio 0.99.3