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| treeman-package | Phylogenetic Tree Manipulation |
| addTip | Add tip to a tree |
| as-TreeMen | Convert list to a TreeMen |
| as.character-method | Node-class |
| as.character-method | TreeMan-class |
| as.character-method | TreeMen-class |
| 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 |
| cTrees-method | TreeMan-class |
| cTrees-method | TreeMen-class |
| 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 |
| Node-method | Node-class |
| pinTips | Pin tips to a tree |
| print-method | Node-class |
| print-method | TreeMan-class |
| print-method | TreeMen-class |
| 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 |
| show-method | Node-class |
| show-method | TreeMan-class |
| show-method | TreeMen-class |
| str-method | TreeMan-class |
| str-method | TreeMen-class |
| treeman | Phylogenetic Tree Manipulation |
| TreeMan-class | TreeMan-class |
| TreeMan-method | TreeMan-class |
| TreeMen-class | TreeMen-class |
| TreeMen-method | TreeMen-class |
| viz | Method viz |
| viz-method | Method viz |
| writeTree | Write a Newick tree |
| [-method | Node-class |
| [-method | TreeMan-class |
| [-method | TreeMen-class |
| [[-method | TreeMan-class |
| [[-method | TreeMen-class |