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treeman

An R package for manipulating phylogentic trees using an intuitive S4 class structure.

The treeman R package provides a list based class for encoding phylogenetic trees in R, making manipulating phylogenetic trees easier to code and more efficient to run. treeman is aimed to be fast, simple and intuitive.

Installation

With CRAN:

install.packages('treeman')

Installing the development copy via GitHub

library(devtools)
install_github('dombennett/treeman')

Quick guide

# working with the TreeMan class
library(treeman)
?TreeMan  # check the documentation
tree <- randTree(10)  # generate a random tree of 10 tips
summary(tree)  # check key stats
tree["tips"]  # extract key stats

For more details check out the wiki.

Licence

GPL-2

Status

Version 1.1 released.

Reference

Bennett, D.J., Sutton, M.D. & Turvey, S.T., 2017. treeman: an R package for efficient and intuitive manipulation of phylogenetic trees. BMC Research Notes, 10(1), p.30. Available online

Author

D.J. Bennett (but I welcome pull requests!)

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Version

Install

install.packages('treeman')

Monthly Downloads

74

Version

1.1.4

License

GPL-2

Maintainer

Last Published

May 26th, 2020

Functions in treeman (1.1.4)

TreeMan-to-phylo

Convert TreeMan to phylo

Add tip to a tree

TreeMen-to-multiPhylo

Convert TreeMen to multiPhylo

Phylogenetic tree of Aves

Add clade to tree

Generate a balanced tree

Add node matrix to a tree

Get extant tips from a tree

Calculate phylogenetic diversity

Get extinct tips from a tree

Get a node slot

Get all nodes connected by given tips

Calculate phylogenetic overlap

Calculate the BLD between two trees

Get pre-nodes to root

Calculate the distance matrix

Get a node slot for multiple nodes

Get post-nodes to tips

Calculate the triplet distance between two trees

Calculate evolutionary distinctness for part of tree

Get path between nodes

Calculate the balances of all nodes

Calculate the balance of a node

Check if ndlst is correct

Get ages for multiple nodes

getNdsFrmTxnyms

Get IDs for nodes represented txnyms

Get children IDs for multiple nodes

Calculate evolutionary distinctness

multiPhylo-to-TreeMen

Convert multiPhylo to TreeMen

Get unique nodes represented by tips

Write a .trmn tree

Check if trees are correct

Save a TreeMan object in serialization format

Calculate the Robinson-Foulds distance between two trees

fastCheckTreeMan

Check if tree is correct, fast!

Get node labels based on online taxonomic database

Get children IDs

Is tree ultrametric?

list-to-TreeMen

Convert list to a TreeMen

Get phylogenetic diversity of node

Get pre-distance

Load a TreeMan object in serialization format

Get the sets of labels for each bipartition in tree

phylo-to-TreeMan

Convert phylo to TreeMan

Remove node matrix

Pin tips to a tree

Get age of tree

Set the age of a tree

Get post-nodes to tips for multiple nodes

Get pre-nodes for multiple nodes

Get pre-distances

Get age ranges for multiple nodes

Get phylogenetic diversities of nodes

Set the ID of a node

Get lineage for multiple nodes

Read a .trmn tree

Phylogenetic tree of European Flora

Update prinds and tinds

Remove a clade from a tree

Phylogenetic tree of Mammalia

Set the branch lengths of specific nodes

Set the phylogenetic diversity

Remove nodes from a tree

treeman-package

Phylogenetic Tree Manipulation

Update tree slots after manipulation

Generate a tree of two tips

Set the IDs of multiple nodes

Set a user defined slot for multiple nodes

Write a Newick tree

multiPhylo-class

multiPhylo class

Generate an unbalanced tree

Set the branch length of a specific node

Make tree ultrametric

Set a user defined slot

Remove a user-defined slot

Generate a random tree

Remove tips from a tree

Read a Newick tree

Set the txnym slots in a tree

Resolve taxonmic names online