treeman: Phylogenetic Tree Manipulation Class and Methods

S4 class and methods for efficient phylogenetic tree manipulation for simulating evolution, running phylogenetic statistics and plotting.

Install the latest version of this package by entering the following in R:
install.packages("treeman")
AuthorD.J. Bennett
Date of publication2016-04-17 19:50:17
MaintainerD.J. Bennett <dominic.john.bennett@gmail.com>
LicenseGPL-2
Version1.0

View on CRAN

Man pages

addTip: Add tip to a tree

as-TreeMen: Convert list to a TreeMen

calcDstBLD: Calculate the BLD between two trees

calcDstMtrx: Calculate the distance matrix

calcDstRF: Calculate the Robinson-Foulds distance between two trees

calcDstTrp: Calculate the triplet distance between two trees

calcFrPrp: Calculate evolutionary distinctness

calcNdBlnc: Calculate the balance of a node

calcNdsBlnc: Calculate the balances of all nodes

calcOvrlp: Calculate phylogenetic overlap

calcPhyDv: Calculate phylogenetic diversity

cTrees: cTrees

getNdAge: Get age

getNdKids: Get children IDs

getNdLng: Get lineage

getNdPrid: Get pre-nodes to root

getNdPtid: Get post-nodes to tips

getNdsAge: Get ages for multiple nodes

getNdsKids: Get children IDs for multiple nodes

getNdsLng: Get lineage for multiple nodes

getNdSlt: Get a node slot

getNdsPrid: Get pre-nodes to root for multiple nodes

getNdsPtid: Get post-nodes to tips for multiple nodes

getNdsSlt: Get a node slot for multiple nodes

getNdsSstr: Get sister id

getNdSstr: Get sister id

getOtgrp: Get outgroup

getPath: Get path between nodes

getPrnt: Get parent

getSpnAge: Get age range

getSpnsAge: Get age ranges for multiple nodes

getSubtree: Get subtree

getTxnyms: Get node id(s) for txonyms

mammals: Phylogenetic tree of Mammalia

Node-class: Node-class

pinTips: Pin tips to a tree

randTree: Generate a random tree

readTree: Read a Newick tree

rmTip: Remove tip from a tree

setAge: Set the age of a tree

setNdID: Set the ID of a node

setNdOther: Set a user defined slot

setNdsID: Set the IDs of multiple nodes

setNdsOther: Set a user defined slot for multiple nodes

setNdSpn: Set the branch length of a specific node

setNdsSpn: Set the branch lengths of specific nodes

setPD: Set the phylogenetic diversity

setTol: Set the extinction tolerance

TreeMan-class: TreeMan-class

TreeMan-method: Method viz

treeman-package: Phylogenetic Tree Manipulation

TreeMen-class: TreeMen-class

writeTree: Write a Newick tree

Functions

addTip Man page
as.character,Node-method Man page
as.character,TreeMan-method Man page
as.character,TreeMen-method Man page
as-TreeMen Man page
calcDstBLD Man page
calcDstMtrx Man page
calcDstRF Man page
calcDstTrp Man page
calcFrPrp Man page
calcNdBlnc Man page
calcNdsBlnc Man page
calcOvrlp Man page
calcPhyDv Man page
cTrees Man page
cTrees,TreeMan-method Man page
cTrees,TreeMen-method Man page
getNdAge Man page
getNdKids Man page
getNdLng Man page
getNdPrid Man page
getNdPtid Man page
getNdsAge Man page
getNdsKids Man page
getNdsLng Man page
getNdSlt Man page
getNdsPrid Man page
getNdsPtid Man page
getNdsSlt Man page
getNdsSstr Man page
getNdSstr Man page
getOtgrp Man page
getPath Man page
getPrnt Man page
getSpnAge Man page
getSpnsAge Man page
getSubtree Man page
getTxnyms Man page
mammals Man page
[,Node,character-method Man page
Node-class Man page
Node-method Man page
pinTips Man page
print,Node-method Man page
print,TreeMan-method Man page
print,TreeMen-method Man page
randTree Man page
readTree Man page
rmTip Man page
setAge Man page
setNdID Man page
setNdOther Man page
setNdsID Man page
setNdsOther Man page
setNdSpn Man page
setNdsSpn Man page
setPD Man page
setTol Man page
show,Node-method Man page
show,TreeMan-method Man page
show,TreeMen-method Man page
str,TreeMan-method Man page
str,TreeMen-method Man page
treeman Man page
[,TreeMan,character-method Man page
[[,TreeMan,character-method Man page
TreeMan-class Man page
TreeMan-method Man page
treeman-package Man page
[[,TreeMen,ANY-method Man page
[,TreeMen,character-method Man page
TreeMen-class Man page
TreeMen-method Man page
viz Man page
viz,TreeMan-method Man page
writeTree Man page

Files

tests
tests/testthat
tests/testthat/test-get-methods.R tests/testthat/test-update-methods.R tests/testthat/test-set-methods.R tests/testthat/test-node.R tests/testthat/test-rw-methods.R tests/testthat/test-treemen.R tests/testthat/test-treeman.R tests/testthat/test-display-methods.R tests/testthat/test-manip-methods.R tests/testthat/test-gen-methods.R tests/testthat/test-calc-methods.R tests/test-all.R
NAMESPACE
data
data/mammals.rda
R
R/manip-methods.R R/update-methods.R R/node-declaration.R R/treeman-declaration.R R/calc-methods.R R/read-write-methods.R R/set-methods.R R/gen-methods.R R/treemen-declaration.R R/get-methods.R R/zzz.R
README.md
MD5
DESCRIPTION
man
man/getSubtree.Rd man/getNdSlt.Rd man/getNdsAge.Rd man/TreeMen-class.Rd man/addTip.Rd man/getSpnsAge.Rd man/mammals.Rd man/getNdsPrid.Rd man/calcNdBlnc.Rd man/TreeMan-class.Rd man/getNdLng.Rd man/getNdPtid.Rd man/as-TreeMen.Rd man/setTol.Rd man/getNdPrid.Rd man/getNdsSlt.Rd man/getOtgrp.Rd man/getSpnAge.Rd man/calcDstBLD.Rd man/getNdKids.Rd man/writeTree.Rd man/randTree.Rd man/Node-class.Rd man/setNdsSpn.Rd man/getTxnyms.Rd man/calcDstTrp.Rd man/getNdsKids.Rd man/cTrees.Rd man/calcFrPrp.Rd man/readTree.Rd man/treeman-package.Rd man/setNdOther.Rd man/rmTip.Rd man/TreeMan-method.Rd man/calcDstMtrx.Rd man/setNdsID.Rd man/setAge.Rd man/calcNdsBlnc.Rd man/calcDstRF.Rd man/getNdAge.Rd man/setNdSpn.Rd man/getPath.Rd man/getNdsLng.Rd man/getNdsPtid.Rd man/calcPhyDv.Rd man/getNdsSstr.Rd man/getNdSstr.Rd man/setNdsOther.Rd man/calcOvrlp.Rd man/pinTips.Rd man/getPrnt.Rd man/setNdID.Rd man/setPD.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.