treeman: Phylogenetic Tree Manipulation Class and Methods

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

Author
D.J. Bennett
Date of publication
2016-04-17 19:50:17
Maintainer
D.J. Bennett <dominic.john.bennett@gmail.com>
License
GPL-2
Version
1.0

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