# Phylogenetic Tree Manipulation Class and Methods

## Documentation for package ‘treeman’ version 1.1.4

- DESCRIPTION file.

## Help Pages

A B C E F G I L M N O P R S T U W misc

treeman-package | Phylogenetic Tree Manipulation

## -- A --

a | TreeMen-class
addClade | Add clade to tree
addNdmtrx | Add node matrix to a tree
addTip | Add tip to a tree
as.character-method | Node-class
as.character-method | TreeMan-class
as.character-method | TreeMen-class

## -- 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 --

Extract | 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 --

isUltrmtrc | 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 --

randTree | Generate a random tree
readTree | Read a Newick tree
readTrmn | Read a .trmn tree
rmClade | Remove a clade from a tree
rmNdmtrx | Remove node matrix
rmNodes | Remove nodes from a tree
rmOtherSlt | Remove a user-defined slot
rmTips | Remove tips from a tree

## -- 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 --

[-method | Node-class
[-method | TreeMan-class
[-method | TreeMen-class
[[-method | TreeMan-class
[[-method | TreeMen-class