yulab.utils::yulab_msg()
for startup message (2024-07-26, Fri)write.beast()
(2024-04-08, Mon, #113)read.beast()
(2023-12-13, Wed, #118)write.jtree()
(2023-12-13, Wed, #117)write.jplace()
method to export jplace
object to a jplace file (2023-11-27, Mon, #112, #115)as.phylo.hclust_node()
to fix as.phylo.pvclust()
issue (2023-8-25, Fri, #110)find.hclust.igraph()
method to hierarchical clustering graph nodes (2023-08-11, Fri, #105) spt()
and as.phylo.igraph()
to consider edge attributes (#105)spt
method to find shortest path tree (2023-07-14, Fri, #102)citEntry()
to bibentry()
(2023-07-14, Fri, #102)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)read.nhx()
when metadata contains both character and numeric (e.g., AAA111) (2023-05-31, Wed, #97)dendro
object (output of ggdendro::dendro_data()
) to a phylo object (2023-03-02, Thu, #95)inner_join()
method to allows appending data of a variabletidyr::unnest
can extract and convert the data to a simple tibble data frame (#93)by = c( 'columnX' = 'cloumnY')
data.frame
that are not presented in the treeas.phylo
and as.treedata
for data.frame object (2022-10-31, Mon, #88)as.phylo()
method for list
(2022-09-14, Wed, #86)as.treedata.pvclust
method (2022-08-15, Mon, #82)read.nextstrain.json()
function to parse json tree file from NextStrain (2022-08-03, Wed, #81)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)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)groupClade.treedata
to return a treedata
object instead of phylo
(2021-11-12, Fri)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)force.ultrametric
parameter in read.mcmctree
read.mcmctree
for PAML MCMCTree result (2021-06-04, Fri)read.nhx
for large tree file (2021-03-12, Fri)read.beast.newick
and write.beast.newick
for importing and exporting newick text with metadata in BEAST style (2021-03-11, Thu)%<>%
as it throw error of 'Error: could not find function "%>%<-"' (2020-11-19, Thu) as_tibble
for pvclust
(2020-06-22, Mon)as.phylo
and as.treedata
methods for pvclust
object (2020-06-21, Sun)read.phyloxml
(2019-12-05, Thu)offspring
return integer(0)
instead of throw error if input .node
is a tip (2019-11-21, Thu)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,
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)rename_taxa
now use 1st column as key and 2nd column as value by default (2019-05-28, Tue)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)ape::root.phylo
for compatibility (2019-05-20, Mon)rescale_tree
from ggtree
(2019-01-11, Fri)MRCA
methods for phylo
and treedata
(2019-01-10, Thu)root
method from ggtree::reroot
(2018-12-28, Fri)root
for importing ape::root
generictibble
v=2.0.0 (2018-11-29, Thu)read.jplace
compatible with output of TIPars (2018-08-07, Tue)as.phylo.ggtree
and as.treedata.ggtree
(2018-07-19, Thu)tree_subset
by using rlang::quo
and import utils::head
and utils::tail
(2018-05-24, Thu)tree_subset
methods contributed by @tbradley1013drop.tip
works with tree@extraInfo
(2018-05-23, Wed)groupOTU.treedata
(2018-05-23, Wed)phylo
and treedata
object, now
ggtree
can be used to visualize all tree-like graph. (2018-04-23, Mon)seq_len
and seq_along
read.jtree
and write.jtree
functionsread.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
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