treeman: Phylogenetic Tree Manipulation Class and Methods

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

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

Files in this package

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

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

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