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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

24

Version

1.1.3

License

GPL-2

Maintainer

DJ Bennett

Last Published

September 17th, 2018

Functions in treeman (1.1.3)

TreeMan-to-phylo

Convert TreeMan to phylo

Calculate phylogenetic overlap

Calculate phylogenetic diversity

Check if trees are correct

fastCheckTreeMan

Check if tree is correct, fast!

Get children IDs

Get path between nodes

list-to-TreeMen

Convert list to a TreeMen

Load a TreeMan object in serialization format

multiPhylo-to-TreeMen

Convert multiPhylo to TreeMen

Phylogenetic tree of Aves

Generate a balanced tree

Calculate the triplet distance between two trees

Calculate evolutionary distinctness

Get age of tree

Get the sets of labels for each bipartition in tree

Get children IDs for multiple nodes

TreeMen-to-multiPhylo

Convert TreeMen to multiPhylo

Remove node matrix

Get lineage for multiple nodes

Calculate the BLD between two trees

Add clade to tree

Get all nodes connected by given tips

Remove nodes from a tree

Calculate the distance matrix

Get extinct tips from a tree

Calculate the Robinson-Foulds distance between two trees

Get a node slot

Set the txnym slots in a tree

Get ages for multiple nodes

getNdsFrmTxnyms

Get IDs for nodes represented txnyms

phylo-to-TreeMan

Convert phylo to TreeMan

Get phylogenetic diversities of nodes

Pin tips to a tree

Get pre-distances

Phylogenetic tree of European Flora

Set a user defined slot

Get age ranges for multiple nodes

Resolve taxonmic names online

Update prinds and tinds

Write a .trmn tree

Remove tips from a tree

Remove a user-defined slot

Calculate the balance of a node

Calculate the balances of all nodes

Phylogenetic tree of Mammalia

Add node matrix to a tree

Set the branch length of a specific node

Make tree ultrametric

Generate an unbalanced tree

Add tip to a tree

Calculate evolutionary distinctness for part of tree

Check if ndlst is correct

Get pre-nodes to root

Update tree slots after manipulation

Write a Newick tree

multiPhylo-class

multiPhylo class

Generate a random tree

Get post-nodes to tips

Read a Newick tree

Get extant tips from a tree

Get a node slot for multiple nodes

Get phylogenetic diversity of node

Get pre-distance

Get pre-nodes for multiple nodes

Set the age of a tree

Get post-nodes to tips for multiple nodes

Set the ID of a node

Get unique nodes represented by tips

Is tree ultrametric?

Read a .trmn tree

Remove a clade from a tree

Save a TreeMan object in serialization format

Set the IDs of multiple nodes

Set the branch lengths of specific nodes

Set the phylogenetic diversity

Get node labels based on online taxonomic database

Set a user defined slot for multiple nodes

treeman-package

Phylogenetic Tree Manipulation

Generate a tree of two tips