Man pages for treeman
Phylogenetic Tree Manipulation Class and Methods
| addClade | Add clade to tree |
| addNdmtrx | Add node matrix to a tree |
| addTip | Add tip to a tree |
| birds | Phylogenetic tree of Aves |
| blncdTree | Generate a balanced tree |
| 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 |
| fastCheckTreeMan | Check if tree is correct, fast! |
| 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 |
| isUltrmtrc | Is tree ultrametric? |
| list-to-TreeMen | Convert list to a TreeMen |
| loadTreeMan | Load a TreeMan object in serialization format |
| mammals | Phylogenetic tree of Mammalia |
| multiPhylo-class | multiPhylo class |
| multiPhylo-to-TreeMen | Convert multiPhylo to TreeMen |
| Node-class | Node-class |
| phylo-class | phylo class |
| phylo-to-TreeMan | Convert phylo to TreeMan |
| pinTips | Pin tips to a tree |
| plants | Phylogenetic tree of European Flora |
| pstMnp | Update prinds and tinds |
| 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 |
| 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 |
| taxaResolve | Resolve taxonmic names online |
| TreeMan-class | TreeMan-class |
| treeman-package | Phylogenetic Tree Manipulation |
| TreeMan-to-phylo | Convert TreeMan to phylo |
| TreeMen-class | TreeMen-class |
| TreeMen-to-multiPhylo | Convert TreeMen to multiPhylo |
| twoer | Generate a tree of two tips |
| ultrTree | Make tree ultrametric |
| unblncdTree | Generate an unbalanced tree |
| updateSlts | Update tree slots after manipulation |
| writeTree | Write a Newick tree |
| writeTrmn | Write a .trmn tree |
