treeman v1.1.4

0

Monthly downloads

0th

Percentile

Phylogenetic Tree Manipulation Class and Methods

S4 class and methods for intuitive and efficient phylogenetic tree manipulation.

Readme

treeman

Build StatusCoverage StatusCRAN downloadsRdoc

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!)

Functions in treeman

Name Description
TreeMan-to-phylo Convert TreeMan to phylo
addTip Add tip to a tree
Node-class Node-class
TreeMen-to-multiPhylo Convert TreeMen to multiPhylo
birds Phylogenetic tree of Aves
TreeMen-class TreeMen-class
TreeMan-class TreeMan-class
addClade Add clade to tree
blncdTree Generate a balanced tree
addNdmtrx Add node matrix to a tree
cTrees cTrees
getLvng Get extant tips from a tree
calcPhyDv Calculate phylogenetic diversity
getDcsd Get extinct tips from a tree
getNdSlt Get a node slot
getCnnctdNds Get all nodes connected by given tips
calcOvrlp Calculate phylogenetic overlap
calcDstBLD Calculate the BLD between two trees
getNdPrids Get pre-nodes to root
getNdAge Get age
calcDstMtrx Calculate the distance matrix
getNdsSlt Get a node slot for multiple nodes
getNdPtids Get post-nodes to tips
getNdsSstr Get sister id
calcDstTrp Calculate the triplet distance between two trees
calcPrtFrPrp Calculate evolutionary distinctness for part of tree
getPath Get path between nodes
calcNdsBlnc Calculate the balances of all nodes
calcNdBlnc Calculate the balance of a node
getOtgrp Get outgroup
checkNdlst Check if ndlst is correct
getNdsAge Get ages for multiple nodes
getNdsFrmTxnyms Get IDs for nodes represented txnyms
getNdsKids Get children IDs for multiple nodes
calcFrPrp Calculate evolutionary distinctness
getNdSstr Get sister id
multiPhylo-to-TreeMen Convert multiPhylo to TreeMen
getUnqNds Get unique nodes represented by tips
writeTrmn Write a .trmn tree
checkTreeMen Check if trees are correct
saveTreeMan Save a TreeMan object in serialization format
phylo-class phylo class
calcDstRF Calculate the Robinson-Foulds distance between two trees
fastCheckTreeMan Check if tree is correct, fast!
searchTxnyms Get node labels based on online taxonomic database
getNdKids Get children IDs
isUltrmtrc Is tree ultrametric?
list-to-TreeMen Convert list to a TreeMen
getNdPD Get phylogenetic diversity of node
getNdPrdst Get pre-distance
loadTreeMan Load a TreeMan object in serialization format
getBiprts Get the sets of labels for each bipartition in tree
phylo-to-TreeMan Convert phylo to TreeMan
rmNdmtrx Remove node matrix
pinTips Pin tips to a tree
getAge Get age of tree
getNdLng Get lineage
setAge Set the age of a tree
getNdsPtids Get post-nodes to tips for multiple nodes
getSpnAge Get age range
getNdsPrids Get pre-nodes for multiple nodes
getPrnt Get parent
getSubtree Get subtree
getNdsPrdst Get pre-distances
getSpnsAge Get age ranges for multiple nodes
getNdsPD Get phylogenetic diversities of nodes
setNdID Set the ID of a node
getNdsLng Get lineage for multiple nodes
readTrmn Read a .trmn tree
plants Phylogenetic tree of European Flora
pstMnp Update prinds and tinds
rmClade Remove a clade from a tree
mammals Phylogenetic tree of Mammalia
setNdsSpn Set the branch lengths of specific nodes
setPD Set the phylogenetic diversity
rmNodes Remove nodes from a tree
treeman-package Phylogenetic Tree Manipulation
updateSlts Update tree slots after manipulation
twoer Generate a tree of two tips
setNdsID Set the IDs of multiple nodes
setNdsOther Set a user defined slot for multiple nodes
writeTree Write a Newick tree
multiPhylo-class multiPhylo class
unblncdTree Generate an unbalanced tree
setNdSpn Set the branch length of a specific node
ultrTree Make tree ultrametric
setNdOther Set a user defined slot
rmOtherSlt Remove a user-defined slot
randTree Generate a random tree
rmTips Remove tips from a tree
readTree Read a Newick tree
setTxnyms Set the txnym slots in a tree
taxaResolve Resolve taxonmic names online
No Results!

Last month downloads

Details

Type Package
License GPL-2
RoxygenNote 7.0.2
Collate 'calc-methods.R' 'check_methods.R' 'cnvrt-methods.R' 'gen-methods.R' 'get-nd-methods.R' 'get-nds-methods.R' 'get-spcl-methods.R' 'manip-methods.R' 'ndlst-methods.R' 'ndmtrx-methods.R' 'node-declaration.R' 'read-write-methods.R' 'server-methods.R' 'set-methods.R' 'treeman-declaration.R' 'treemen-declaration.R' 'update-methods.R' 'viz-methods.R' 'zzz.R'
NeedsCompilation yes
Packaged 2020-05-26 17:31:36 UTC; domben
Repository CRAN
Date/Publication 2020-05-26 22:40:02 UTC

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/treeman)](http://www.rdocumentation.org/packages/treeman)