NEWS
treeio 1.29.1
- use
yulab.utils::yulab_msg()
for startup message (2024-07-26, Fri)
- support treetime output (2024-07-18, Thu)
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
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)
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)
treeio 1.15.4
- support parsing tree qza file from qiime2 (2020-03-01, Mon)
treeio 1.15.3
- support parsing phyloxml (2021-02-04, Thu)
treeio 1.15.2
- bug fixed of parsing nhx, now compatible with missing nhx tag (2020-11-19, Thu)
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)
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,
offspringand
rootnodemethods for
treedata` (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
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
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)
treeio 1.5.1
- bug fixed of
groupOTU.treedata
(2018-05-23, Wed)
treeio 1.4.0
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)
- read.astral (2018-04-17, Tue)
- read.iqtree
treeio 1.3.13
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)
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
- 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>
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>