treeman: Phylogenetic Tree Manipulation Class and Methods
Version 1.0

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

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

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

Node-class Man page
Node-method Man page
TreeMan-class Man page
TreeMan-method Man page
TreeMen-class Man page
TreeMen-method Man page
[,Node,character-method Man page
[,TreeMan,character-method Man page
[,TreeMen,character-method Man page
[[,TreeMan,character-method Man page
[[,TreeMen,ANY-method Man page
addRoot Source code
addTip Man page Source code
as-TreeMen Man page
as.character,Node-method Man page
as.character,TreeMan-method Man page
as.character,TreeMen-method Man page
blncdTree Source code
cMenToAny Source code
cMenToMan Source code
cMenToMen Source code
cTreeObjs Source code
cTrees Man page
cTrees,TreeMan-method Man page
cTrees,TreeMen-method Man page
calcDstBLD Man page Source code
calcDstMtrx Man page Source code
calcDstRF Man page Source code
calcDstTrp Man page Source code
calcFrPrp Man page Source code
calcNdBlnc Man page Source code
calcNdsBlnc Man page Source code
calcOvrlp Man page Source code
calcPhyDv Man page Source code
checkTreeMan Source code
checkTreeMen Source code
dwndateKids Source code
dwndateNd Source code
dwndateTip Source code
getIDandSpn Source code
getNdAge Man page Source code
getNdKids Man page Source code
getNdLng Man page Source code
getNdPrid Man page Source code
getNdPtid Man page Source code
getNdSlt Man page Source code
getNdSstr Man page Source code
getNdsAge Man page Source code
getNdsKids Man page Source code
getNdsLng Man page Source code
getNdsPrid Man page Source code
getNdsPtid Man page Source code
getNdsSlt Man page Source code
getNdsSstr Man page Source code
getOtgrp Man page Source code
getPath Man page Source code
getPrid Source code
getPrnt Man page Source code
getRdrEnv Source code
getSpnAge Man page Source code
getSpnsAge Man page Source code
getSubtree Man page Source code
getTxnyms Man page Source code
globalUpdateAll Source code
globalUpdateKids Source code
imblncdTree Source code
mammals Man page
mkNd Source code
mkNdLst Source code
newNd Source code
pinTips Man page Source code
print,Node-method Man page
print,TreeMan-method Man page
print,TreeMen-method Man page
randTree Man page Source code
readTree Man page Source code Source code
rmTip Man page Source code
setAge Man page Source code
setNdID Man page Source code
setNdOther Man page Source code
setNdSpn Man page Source code
setNdTxnym Source code
setNdsID Man page Source code
setNdsOther Man page Source code
setNdsSpn Man page Source code
setNdsTxnym Source code
setPD Man page Source code
setRoot Source code
setTol Man page Source code
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-package Man page
updateKids Source code
updateNd Source code
updateNdsSlt Source code
updateTip Source code
updateTreeSlts Source code
viz Man page
viz,TreeMan-method Man page
writeTree Man page Source code

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
treeman documentation built on May 19, 2017, 8:33 p.m.