A Tidy Tool for Phylogenetic Tree Data Manipulation

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.


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Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. ‘tidytree’ provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

Author

Guangchuang YU

School of Basic Medical Sciences, Southern Medical University

https://guangchuangyu.github.io

saythanks

Installation

Get the released version from CRAN:

install.packages("tidytree")

Or the development version from github:

## install.packages("devtools")
devtools::install_github("GuangchuangYu/tidytree")

News

tidytree 0.2.4

  • 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

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

tidytree 0.2.2

tidytree 0.2.1

tidytree 0.2.0

  • 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

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

tidytree 0.1.8

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

tidytree 0.1.7

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

Reference manual

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install.packages("tidytree")

0.2.4 by Guangchuang Yu, 3 months ago


https://github.com/GuangchuangYu/tidytree


Report a bug at https://github.com/GuangchuangYu/tidytree/issues


Browse source code at https://github.com/cran/tidytree


Authors: Guangchuang Yu [aut, cre, cph] , Bradley Jones [ctb] , Zebulun Arendsee [ctb]


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


Artistic-2.0 license


Imports ape, dplyr, lazyeval, magrittr, methods, rlang, tibble, utils

Suggests ggtree, knitr, prettydoc, testthat, treeio


Imported by oppr.


See at CRAN