Phylogenetic Tree Manipulation Class and Methods

Documentation for package ‘treeman’ version 1.1.4

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Phylogenetic Tree Manipulation

-- A --

-- B --

birds	Phylogenetic tree of Aves
blncdTree	Generate a balanced tree

-- C --

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
calcPrtFrPrp	Calculate evolutionary distinctness for part of tree
checkNdlst	Check if ndlst is correct
checkTreeMen	Check if trees are correct
cTrees	cTrees
cTrees-method	TreeMan-class
cTrees-method	TreeMen-class

-- E --

TreeMen-class

-- F --

fastCheckTreeMan	Check if tree is correct, fast!
from	TreeMen-class

-- G --

getAge	Get age of tree
getBiprts	Get the sets of labels for each bipartition in tree
getCnnctdNds	Get all nodes connected by given tips
getDcsd	Get extinct tips from a tree
getLvng	Get extant tips from a tree
getNdAge	Get age
getNdKids	Get children IDs
getNdLng	Get lineage
getNdPD	Get phylogenetic diversity of node
getNdPrdst	Get pre-distance
getNdPrids	Get pre-nodes to root
getNdPtids	Get post-nodes to tips
getNdsAge	Get ages for multiple nodes
getNdsFrmTxnyms	Get IDs for nodes represented txnyms
getNdsKids	Get children IDs for multiple nodes
getNdsLng	Get lineage for multiple nodes
getNdSlt	Get a node slot
getNdsPD	Get phylogenetic diversities of nodes
getNdsPrdst	Get pre-distances
getNdsPrids	Get pre-nodes for multiple nodes
getNdsPtids	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
getUnqNds	Get unique nodes represented by tips

-- I --

Is tree ultrametric?

-- L --

list	TreeMen-class
list-to-TreeMen	Convert list to a TreeMen
loadTreeMan	Load a TreeMan object in serialization format

-- M --

mammals	Phylogenetic tree of Mammalia
multiPhylo	multiPhylo class
multiPhylo-class	multiPhylo class
multiPhylo-to-TreeMen	Convert multiPhylo to TreeMen

-- N --

Node-class	Node-class
Node-method	Node-class

-- O --

of	TreeMen-class

-- P --

phylo	phylo class
phylo-class	phylo class
phylo-to-TreeMan	Convert phylo to TreeMan
pinTips	Pin tips to a tree
plants	Phylogenetic tree of European Flora
print-method	Node-class
print-method	TreeMan-class
print-method	TreeMen-class
pstMnp	Update prinds and tinds

-- R --

-- S --

saveTreeMan	Save a TreeMan object in serialization format
searchTxnyms	Get node labels based on online taxonomic database
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
setTxnyms	Set the txnym slots in a tree
show-method	Node-class
show-method	TreeMan-class
show-method	TreeMen-class
slots	TreeMen-class
str-method	TreeMan-class
str-method	TreeMen-class
summary-method	Node-class
summary-method	TreeMan-class
summary-method	TreeMen-class

-- T --

taxaResolve	Resolve taxonmic names online
treeman	Phylogenetic Tree Manipulation
TreeMan-class	TreeMan-class
TreeMan-method	TreeMan-class
TreeMan-to-phylo	Convert TreeMan to phylo
TreeMen-class	TreeMen-class
TreeMen-method	TreeMen-class
TreeMen-to-multiPhylo	Convert TreeMen to multiPhylo
trees	TreeMen-class
twoer	Generate a tree of two tips

-- U --

ultrTree	Make tree ultrametric
unblncdTree	Generate an unbalanced tree
updateSlts	Update tree slots after manipulation

-- W --

writeTree	Write a Newick tree
writeTrmn	Write a .trmn tree

-- misc --