NEWS

---

tidytree 0.4.6.002

• deprecate random_ref() and use yulab.utils::yulab_msg() (2024-07-26, Fri)
• Ntip() method for 'treedataList' object (2024-04-08, Mon)

tidytree 0.4.6 (2023-12-12)

• import methods::setClassUnion() to fix R check (2023-12-12, Tue)
• check before setOldClass(), which suppose to fix the #47 issue (2023-11-29, Wed)

tidytree 0.4.5 (2023-08-10)

• mv tree operation functions (e.g., parent(), child(), tree_subset(), etc.) from the 'treeio' package (2023-08-03, Thu, #44)
• update valid.edge() to avoid warning (2023-7-18, Tue)

tidytree 0.4.4 (2023-07-15)

• update old-style 'CITATION' from citEntry() to bibentry() (2023-07-14, Fri, #38)
• update dplyr-verb for 'tbl_tree' object to print information to avoid confusion (2023-07-13, Thu, #37, #39)
• add accessor function of node label for 'tbl_tree', 'phylo' and 'treedata' object (2023-07-13, Thu, #37)

tidytree 0.4.3

• add print() method for 'tbl_tree' object to avoid confusion with tbl_df (2023-07-12, Wed)

tidytree 0.4.2 (2022-12-18)

• fixed the dots issue of left_join (2022-12-16, Fri, #30, #31)

tidytree 0.4.1 (2022-09-26)

• update citation with the ggtree imeta paper (2022-08-13, Sat)

tidytree 0.4.0 (2022-08-13)

• update citation with the tree data book (2022-08-13, Sat)

tidytree 0.3.9 (2022-03-04)

• update package startup message (2022-03-04, Fri)

tidytree 0.3.8 (2022-02-17)

• add the CRC book in startup message (2022-02-17, Thu)

tidytree 0.3.7 (2022-01-10)

• update startup message to randomly print two citation items of the ggtree package suite (2022-01-10, Mon)

tidytree 0.3.6 (2021-11-12)

• use yulab.utils::str_wrap to print tree (2021-10-09, Sat)

tidytree 0.3.5 (2021-09-08)

• add select, filter, mutate, left_join, unnest, pull and rename verbs for treedata object (2021-08-22, Sun; @xiangpin, #19)
• update print and show methods for treedata
  • with options(show_data_for_treedata=TRUE) to control whether show associated data (2021-08-20, Fri; @xiangpin, #18)

tidytree 0.3.4 (2021-05-22)

• implement merge method for tbl_tree object (2020-07-03, Fri)
  • https://github.com/YuLab-SMU/treeio/issues/36
• remove mutate_, filter_ and group_by_ according to the change of dplyr (v=1.0.0) (2020-04-09, Thu)

tidytree 0.3.3 (2020-04-02)

• remove data_frame according to the change of tibble (v=3.0.0)

tidytree 0.3.2 (2020-03-12)

• use tibble instead of data_frame as it was deprecated in tibble (v=3.0.0) (2020-04-02, Thu)
• compatible with dplyr v=1.0.0 (2020-03-12, Thu)
  • https://github.com/YuLab-SMU/tidytree/pull/12
  • https://github.com/YuLab-SMU/tidytree/issues/13

tidytree 0.3.1 (2019-12-14)

• groupOTU: set group from 0 to NA if only root node is in group of 0 (2019-11-25, Mon)

tidytree 0.3.0 (2019-11-21)

• offspring supports a vector of node ids (2019-11-21, Thu)
• bug fixed of nodelab
• filter and select methods for ggtree object (2019-10-31, Thu)

tidytree 0.2.9 (2019-10-28)

• offsprint(tip, self_include=TRUE) will return the input tip (2019-10-06, Sun)

tidytree 0.2.8 (2019-09-27)

• update offspring to compatible with missing nodes, e.g. for tree after ggtree::collapse (2019-09-16, Mon)

tidytree 0.2.7 (2019-09-12)

• allow calling MRCA with only one node and will return the node itself (2019-08-30, Fri)

tidytree 0.2.6 (2019-08-09)

• nodeid and nodelab methods for converting from label to node number and vice versa (2019-08-09, Fri)
• allow determine MRCA of a vector of tips (2019-08-08, Thu)

tidytree 0.2.5 (2019-07-22)

• convert elements of roxygen documentation to markdown (2019-05-05, Thu)

tidytree 0.2.4 (2019-02-27)

• call child.tbl_tree instead of child in offspring, (2019-02-26, Tue) so that it works more robust for data.frame.

tidytree 0.2.3 (2019-01-30)

• more parameter for offspring (2019-01-28, Mon)

tidytree 0.2.2

• mv vignette to treedata-book (2019-01-10, Thu)

tidytree 0.2.1 (2018-12-19)

• mutate.tbl_tree method (2018-12-19, Wed)
  • https://github.com/YuLab-SMU/tidytree/issues/7
• bug fixed in child
  • https://github.com/YuLab-SMU/tidytree/pull/8

tidytree 0.2.0 (2018-11-29)

• compatible with tibble v = 2.0.0 (2018-11-29, Thu)
  • change as_data_frame method to as_tibble since as_data_frame was deprecated in tibble and not exported as generics

tidytree 0.1.9 (2018-06-13)

• as_data_frame.phylo works with phylo$root.edge (2018-06-13, Wed)

tidytree 0.1.8 (2018-04-19)

• force get_tree_data(treedata)$node to be integer (2018-04-19, Thu)

tidytree 0.1.7 (2018-02-27)

• get.data, [ and [[ methods (2018-02-26, Mon)